I think abdomunculum would be the most regular diminutive of abdomen. But it seems a bit difficult to me to give a clear answer because the rules about "proper" diminutive suffixes are often based on the form and gender of the original noun, and I know of no existing diminutives formed on nouns with precisely the same morphological form and gender as abdomen, abdominis. If you get it "wrong," you may at least be able to take some comfort from the knowledge that Romans even criticized one another sometimes for using supposedly malformed diminutives.
Abdomen, abdominis is a neuter noun of the third declension, of the "consonant stem" sub-declension class, with a stem ending in the consonant "n" specifically. My impression is that any of these features might be relevant to the formation of the diminutive.
Words with stems ending in n often take diminutives in -cul-
brianpck's answer to Variations on the diminutive: -olus and -ulus contained a link to a page from Allen and Greenough's Latin Grammar that I consulted to try to answer this question. It says
These diminutive endings are all formed by adding -lus to various stems. [...] -culus comes from -lus added to adjectives in -cus formed from stems in n- and s-: as, iuven-cus, Aurun-cus (cf. Aurunculeius), prís-cus, whence the cu becomes a part of the termination, and the whole ending (-culus) is used elsewhere, but mostly with n- and s- stems, in accordance with its origin.
Usually, ...in- + -cul- = ...uncul-, apparently
The Formation of Latin
Diminutives of Nouns and Adjectives, compiled by Ian Andreas Miller, indicates that stems ending -in- regularly change the vowel and have -un- before -culus/-culum/-cula. cnread's answer mentions homunculus, from homo, hominis, which shows this pattern. There is an interesting note in Miller about the history of this formation saying that the u is analogical:
The -uncul- formation in these diminutives was originally created by adding -culā-, -culo- to stems in -on-, where the -o- became -u- by phonetic change (cf. hunc, earlier honc). Some original stems in -nō- (-on-) later became stems in -in- (e.g. homin-, earlier homon- or homōn-) with nominative singular endings in -ō, and through the power of analogy the -uncul- formation was used with other stems in -in- (e.g. pecten, stem pectin-) and stems in -n- with nominative singular forms in -o (e.g. caro, stem carn-) even if they do not actually have stems in -in- or -on-.
I don't know of any Latin diminutives ending in "...in-cul-" (vinculum is derived from the base vinc-).
Gender of diminutives, and the rarity of -unculum/-munculum
Miller says it is a rule that diminutive nouns derived from third-declension nouns retain the gender of the original noun—which for abdomen is neuter—and take the endings -us, -a or -um according to the usual correspondences between form and gender. So it seems to me that abdomunculum would be most regular.
But I'm not entirely certain about recommending -unculum rather than -unculus as in cnread's answer. There are exceptions to the gender-matching rule; Miller mentions rana > ranunculus. And since most nouns ending in -ō in the nominative are masculine or feminine, -unculus and uncula seem to be much more established in Latin than -unculum as suffixes for deriving diminutive nouns from third-declension n-stems. A Perseus search does turn up some existing nouns ending in -unculum, but none of those results seems to be derived from a third-declension noun with a stem ending in -in-.
That said, there are certainly diminutives ending in -culum with something else before it; for example, corpusculum, from the third-declension neuter noun corpus. So perhaps the scarcity of words ending in -un-culum specifically is just coincidental.
So far, pectunculus from pecten is actually the only example I have seen of a diminutive from a noun ending in -en, -inis. It is masculine, but so is the original noun pecten.
Most Latin nouns that end in -en in the nominative and -inis in the genitive seem to have an "m" before this and are neuter. Wiktionary indicates that many of them have a "noun-forming suffix -men" and lists a number of them; I searched on Perseus for words starting with the stems up to the "m" of around 10 of them (like "agm," "germ," "carm") but I wasn't able to find any diminutive forms with their own entries. Another neuter third-declension with a consonant other than m before -en, -inis is gluten.
I also found a passage in Italian that seems to say that "vimunculum" (which is apparently not attested) would be the expected diminutive form of vimen:
Dal positivo vimen uscirono viminculus, vinculus, vinclus (sic). Da quest'ultimo poi abbiamo fatto vinco a significare quel frutice lento e pieghevole donde usci il verbo vincio, se non anche l'altro vinco.
Quasi superfluo il notare che da vimen neutro sarebbesi più verisimilmente derivato un neutro, qui poi tanto più certo, in quanto il supposto derivato è realmente vinculum, non vinculus. Non sarebbe poi gran fatto probabile una tale derivazione da neutri in -men, non avendosene alcun esempio; e quando poi si dovesse ammettere, sarebbe stato piuttosto vimunculum che viminculus (cfr. pectunculus, dal masch. pecten).
(Archivio Glottologico italiano, Volume 2)
I don't speak Italian, but judging from Google translate and cognates, this seems to say that there are no examples of diminutives of neuter nouns in -men.
Post-classical examples of -munculum from -men neuters
For what it's worth, I was able to find one example of "germunculum" via Google, in Dissertatio inauguralis medica de hominis aetatibus, 1824:
En, amicitiae vagabundae in juventute ortum! en, primum pro firmioribus radicibus amoris in alterum sexum figendis germunculum primum! (§27, p. 41)
"Stamunculum", from stamen, staminis, also seems to have been used, in Hortus Malabaricus.
So at least some other people also seem to have had the same idea as me about how to form the diminutives of words like this, if necessary.
Other sources on diminutive formation in Latin
Some other possibly relevant sources I found that I have not yet got a chance to look through:
Word Formation in the Roman Sermo Plebeius, by Frederic Taber Cooper (1895) -- has a section on "Diminutives" starting on page 164
Cooper cites some articles by "Paucker," one of which had a title that sounded like it might be helpful: "Deminutive mit d. Suffix -c-ulus, a, um"
Zeitschr. f. d. oesterr. Gymn. XXVII, p. 273-284. (="Zeitschrift für die österreichischen Gymnasien") I looked though a Google Books result related to this, and found a long list of words with the suffix "-uncul-" that contained many ending in "-uncula" and "-unculus" but none that I could see ending in "-unculum" aside from those already mentioned that are indexed by Perseus and have entries in Lewis & Short.
