These sentences may be logically compatible with a conditional, causal or any other subordinative reading, but only by contextual inference.
When a sentence leaves out something that is grammatically okay to leave out, it's said to be vague about it. When a sentence is vague about something, it's said to be compatible with any instance of that something. For example, the average Chinese sentence is vague about tense and, as such, will be compatible with any tense. In other words, a tense-less sentence is not being ambiguous about a specific underlying tense that's supposedly been dropped - it's simply vague about it.
In your examples, the absence of a logical connector (such as 如果, 因为, 所以, 就, etc) means that your sentences are vague about the logical connection within them. Again, that means that your sentences may well be compatible with a causal or conditional reading (given the right context), but they do not on their own mean it.
Without context, the most faithful reading of them in English is one that simply uses the connector [and/but]
妈妈昨天喝茶，今天喝咖啡。
Mom had tea yesterday and/but is having coffee today.
妈妈不喝茶，喝咖啡。
Mom isn't having tea and/but is having coffee.
What about pronouns? The sentences above do leave the subject of the second clause implicit. But this time, they're not being vague about it: the subject is heavily implied to be 她 and no other.
This means that when you make the subject explicit again, you're adding contrastive emphasis to something that's implicitly there already. Adding a pronoun for emphasis may mark the two clauses further apart, but it does nothing to cancel out the vagueness of their logical connection.
A possible way to translate the sense of contrast here might be simply to use a stronger adversative, something like [(but) instead]:
妈妈昨天喝茶，她今天喝咖啡。
Mom had tea yesterday but is having coffee today instead.
妈妈不喝茶，她喝咖啡
Mom isn't having tea but is having coffee instead.
Please note that, in all four translations here, each sentence is left as a pair of coordinated clauses. Yes, they may well be logically compatible with a subordinative reading (in a conditional or causal context), but that's not what they actually say. And although adding/omitting the pronoun may mark a more important caesura between their two component clauses, this alone will not change the nature of their logical connection from one of coordination to one of subordination, unless you do add 就 or another such word.
Addendum (in reply to comments):
The reason why the sentence with 不, but not the one with 昨天, feels conditional by default is unlikely to be due to the aspect of the verb in the predicate (eg habitual vs progressive, etc). But, yes, you are right to notice a slight difference. It's just that the different nuance you feel in the sentence with 不 is not one of condition; it's one of disjunction. And disjunction, unlike condition, is still consistent with coordination. What makes the logic of that sentence disjunctive is the mere presence of the word 不, which is usually enough to set one clause in pseudo-conditional opposition to another, whether with 就 (eg 不是咖啡就是茶 = it's either coffee or tea) or without (爱信不信 = believe it or not).
This also explains why you feel that adding a pronoun in between the two clauses will block the default conditional reading of the sentence. What it does is separate the two clauses further apart, thereby bleaching out the sense of disjunction to the point where you're simply left with two bare statements of fact.
To wrap up my answer: adding or omitting pronouns will not change the relationship between the clauses of those two sentences. In both cases, the logic is one of coordination, albeit conjunctive in one and disjunctive in the other. Adding a pronoun in the middle will simply add more internal contrast between the two clauses. The reason why adding a contrastive pronoun makes the sentence with 不 feel more descriptive is because the sense of contrast will block the sense of disjunction.
