For example, is there a semantic difference between the two following sentences?
Lapis descendit ab A ad B unâ horâ.
vs.
Lapis descendit ab A ad B una hora.
This site, e.g., says
The distinction between short and long vowels was grammatically significant, cf. hora hour vs. horâ at (this) hour, now
Is this true?
Lapis descendit ab A ad B unâ horâ.
Lapis descendit ab A ad B una hora.
In the context of comparing these two sentences, there is no difference between “unâ horâ” and “una hora”. They mean the same thing (and should be pronounced the same way): they are purely orthographical variants representing the ablative singular of “una hora” (with the “ablative of time” interpretation). The overall sentence means
A stone descends from A to B in/within one hour.
This example seems to be taken with, a slight modification, from Descartes’ Cogitationes Privatae (which has “Lapis, aiebat, descendit ab A ad B una hora”).
I found this text with a Spanish translation on Google, and I know enough Spanish to be able to tell that it confirms the above English translation:
Una piedra — dijo — desciende de A a B en un hora
(Estudios galileanos, by Alexandre Koyré)
I can think of no sensible interpretation of this sentence with “una hora” interpreted as a nominative rather than an ablative noun phrase.
There are many variations on Latin orthography. It is a language that has existed in many times and places, and different customs have naturally developed.
The source you found refers to an orthographic distinction between “hora hour vs. horâ at (this) hour, now”, but this distinction is not universally observed: it applies only to orthographic traditions that use the circumflex consistently to mark the ablative singular of first-declension nouns. Penelope’s answer to the following question describes the possible uses of the circumflex: Interpretation of circumflex in a poem from 1621
Actually, my impression is that only a minority of writers use the circumflex nowadays. Many popular introductory Latin textbooks, such as Wheelock’s, use macrons instead. Typically, macrons are used to mark all long vowels in a word, not just the grammatically significant ones, so in a text using macrons the distinction between nominative singular and ablative singular would usually be written as hōra vs. hōrā.
And in contexts other than introductory textbooks, many modern writers and readers of Latin prefer text without any diacritical marks at all: no circumflexes and no macrons. In text like this, both the nominative singular and ablative singular are written the same way (“una hora”); you can generally figure out which one is meant by context.
So it all depends on the context. You cannot in general assume that “una hora” is nominative rather than ablative; however, this might be a safe assumption if you observe that the text you are reading consistently uses circumflexes to mark the ablative singular of first-declension nouns.
A similar area of variance in written Latin is the use of j and i vs. just i; e.g. "jam" and "iam" are just different ways of writing the same word.
The circumflex used by some authors to indicate long vowels. I prefer to use the macron: hōra versus hōrā. Some ancient inscriptions used an "apex", a diacritic similar to the modern acute: hórá.
Hōra with a short a is unambiguously nominative, "a time" or "an hour". While hōrā with a long a is unambiguously ablative, "at the time" or "in an hour".
In your example sentence, it's unambiguous that the word is hōrā, because hōra with a short a wouldn't make sense. So even without any markings, it would be read with a long ā.
But there are other situations in which long and short vowels can cause significant ambiguity. For example, a famous graffito (paraphrased):
A. B. amat, sed B. alium amat
A. loves B., but B. loves alium
In this case, the ambiguity is used for humor: alium with a short a means "another man", but ālium with a long ā means "garlic".
Or for a more risqué example:
C. anum amat
C. loves an anus
Anus with a short a (feminine, fourth declension) means "old woman", while ānus with a long ā (masculine, second declension) means the same thing it does in English.
