It's a recurring issue in that Aqua easily purifies many liquids such as swamp water, tea or hot spring water. However, this is never an issue whenever she imbibes alcohol.
Was it ever explained if she only purifies "water-based" liquids or she does have control over what she purifies and never seems to apply it well except for her beloved alcohol? Word of god from the author or a select passage from the light novel address this would be great.
First, Aqua did purify alcohol.
In one of Megumin's spin-off light novel1, Aqua was working as a part-time waitress at the guild's bar. However, once she got scolded and fired by the owner since she purified the alcohol accidentally. That's the reason why she was doing civil engineering work instead in the first episode. (source: [1], [2]:post no. 53 by DPKAszx20, reddit)
This implies that she can't really control her purification power; any liquid that she touches will be purified regardless of her intention. Her character introduction usually mentions this (examples: [3]:Aqua/Power Incontinence, [4], [5])
On the other hand, there's also an important info regarding her purification skill. According to a bonus light-novel for digital publication2, Aqua's natural purification skill power changes depending on her emotion/feeling. When she is in pure emotion, her natural purification power is high, otherwise when she is in "vulgar" mode, its power is low. (source: [1])
However, the mystery of her enjoying alcoholic drinks until drunk is never explained explicitly: was she really enjoying it? did she really drunk? Thus, there are only fan theories:
It is based on her emotion (as mentioned before) (source: [1])
When she's drinking alcoholic drinks, she's exposing her self-desire. This makes her purification power low, and thus she can enjoy it. On the other hand, when she was working as a waitress, she was not engulfed in her self-desire because she didn't want to drink it, and thus she accidentally purified it.
Only liquid that's touched directly gets purified (source: most of her character introductions, [2]: post no. 49 & 50, reddit, reddit, reddit, reddit)
Most of the cases, she touched the liquid with her skin (e.g. Darkness' grape juice). However, it's implied that drinking is safe because the lip is considered as mucous membrane, not skin. The problem is, this also generates more question like how she purified customers' alcoholic drink and Kazuma's tea...
She can't really control it (source: reddit, reddit, reddit)
Which means she was actually drinking plain water, and her being drunk was due to the placebo effect or water intoxication.
Debunked fan theories due to the fact mention here:
She only purifies water-based liquid, and alcohol is not water (source: [2]: post 47 & 48, reddit, reddit, reddit, reddit, reddit, reddit)
Chemically, alcohol is ethanol (C2H6O2), not water (H2O). This means that she probably was drinking pure ethanol instead, which surely made her drunk. (Debunked because she did purify alcohol)
Purification takes some time to work (source: [2]: post 52, reddit, reddit)
Similar to the case when she took a long time to purify a lake, she needed some time to purify her drink. (Debunked because she purified Darkness' grape juice instantly)
Alcohol is considered holy/pure/sacred by many religions (source: reddit, reddit, reddit, reddit)
There are facts about alcohol such as wine is considered sacred. Examples are Jesus turning water into wine, Japanese gods like sake, etc.. (Debunked anyway, since she did purify alcohol)
Finally, the scene where she was drunk and puking rainbow is anime only. It's not mentioned in the light novel, thus might not be considered canon. (source: reddit)
Another thing to ponder: why isn't her bodily fluid got purified? If this is to be considered, then the only theory that works is "Only liquid that's touched directly gets purified".
Sources:
1 The spin-off light novels are officially free to read on Sneaker Bunko (Japanese), but I don't have time to find the related passage. It'd be great if someone can confirm this in the comment.
2 Unfortunately, I can't find the origin of the light-novel mentioned there.