Yes, with some practice there is no difficulty in understanding which is which and of course no reasoning is necessary, otherwise the forms would be unpractical and wouldn’t be used. The clues are easy to identify as far as pronunciation goes, but then you have to know well the gender of the nouns.

Those forms would occur for instance as an answer or a confirmation. I chose this type of occurrence for the examples but the forms occur in plain text too. You can tell whether the pronoun "le" or "la" is being used from the gender of the antecedent and the tense (pronunciation).

• — Vous me dites qu’il a fait son devoir de mathématiques ce soir ?
  — Il l’a fait.

"Devoir" is masculine and so that’s enough here to deduce that the tense is the "passé composé" because "la" wouldn’t make sense.

• — Est-ce qu’il a fait sa rédaction ce soir ?
  — Il la fait.

(Here, we would say rather "Il est en train de la faire." but "Il la fait." is also a possibility that amounts to the same meaning.)

If we suppose the spelling is "l’a" in this second example then we have either an elision of "le" or an elision of "la". "Le" is not a possibility as "le", being masculine (or neuter¹) cannot be used for representing "rédaction" which is feminine. If we suppose it is the elision of "la", then "a" must be the verb "avoir" and "fait" is the past participle of "faire", which is not correct as this past participle has to agree with the cod ("la", here writen "l’"); we should have "Il l’a faite." (here "e" is pronounced) . Therefore the spelling can’t be "l’a".; it’s "la" and the tense is the "présent de l’indicatif".
Of course, after getting used to it you don’t have to go through this reasonning to determine which is which, nor is it ever necessary to do that if you spend enough time reading. I can tell you that I never did; but if you think it helps to go through such an analysis now and again go ahead and do it, it might speed up your learning process.

¹_{— neuter when it stands for what a clause is saying}

I don’t think anyone would be able to distinguish il l’a fait and il la fait phonetically.

In spoken French, the pronoun il is often reduced to a single [i] so both sentences would be pronounced the same way:

Il l’a fait → Y l’a fait → [i.la.fɛ] or [i.la.fe].

Il la fait → Y la fait →            //

On the other hand, a careful pronunciation can lengthen or geminate the L [il:a.fɛ] or [il.la.fɛ] in one or both sentences. This doesn’t help either.

What does prevent these sentences to be ambiguous in the vast majority of cases is the context.

It will tell which meaning is the most likely to match it, the best bet being the first one (il l’a fait) because it is more common.

Il l’a fait, la sieste. (he had a nap)

Il la fait, la sieste. (he is having a nap or he usually has a nap)

Note that I would translate il l’a fait by "he has made it" but either "he made it" or "he did it" while il la fait can be "he makes" or "he does it" with it representing a feminine word.