From fluere, su(short)perfluere means to overflow. However, I'm not sure how the adjective superflu(first u short)us is pronounced. My guess would be that both final Us are short, but why are they not marked so?
The vowel lengths are: sŭpĕrflŭŭs. All four vowels are short.
The nominative singular forms are: sŭpĕrflŭŭs, sŭpĕrflŭă, and sŭpĕrflŭŭm. Based on the endings -us/-a/-um, we can tell that it is short.
The rule is that the nominative masculine singular form cannot end with -ūs, so the shortness is implied and does not need to be marked. In fact, you can only find -ūs in the nominative plural form of the 4th declension.
The second conjugation ending -us descends from o-stem in Old Latin (-os), which is from the o-grade of the Indo-European ablaut.
For example, Proto-Indo-European *pórḱos gives Proto-Italic *porkos, which gives Latin porcus.
As Leaky Nun has said, this word has a short vowel in every syllable: sŭpĕrflŭŭs, or in broad IPA /suˈperfluus/ (in narrower IPA, the pronunciation in the later classical period might have been something like [sʊˈpɛɾfluʊs] or [sʊˈpɛɾflʊʊs]).
You can see the length of the vowel in the penult marked in the Lewis and Short dictionary entry, available online at the Perseus Digital Library. It doesn't mark the quality of the vowel in the final syllable. I believe this information is generally omitted by Lewis and Short when it can be inferred from the declension class, as it can in this case: the -us suffix of the second declension nominative singular always has a short u. (Lewis and Short also omit to mark the length of the "e" in the penult; I assume the reason for this is because it has a "hidden quantity" since the syllable is closed by the coda /r/).
Vowel length is not consistently marked in Latin writing outside of dictionaries (many writers never mark it at all), especially not with breves (macrons for long vowels are somewhat more common, but still not preferred by many in running text).
A general vowel length rule that would be applicable to the penult is that a (monophthongal) vowel before another vowel is usually short in Latin. You can find this rule, along with some exceptions, in Allen and Greenough's New Latin Grammar section 604 on the Allen and Greenough online website. I don't know the historical reasons for it, but it is a good rule of thumb to be aware of.