Only the second one works. The first one is unreal - it means that the situation isn't real or the action won't happen. If you had hand sanitizer = you don't have hand sanitizer. If they had hand sanitizer, I would get one. (they don't have it) The second one is a 'possible' conditional. We don't know that there is hand sanitizer but it is a real possibility. If they have it, I'll get you one. If they don't, I won't. Both forms are used to describe a present or future time. The first one (unreal) uses a past form of the verb to show that the situation is not true, rather than describing a past time. If you want to read more about it, you can search for 'real and unreal conditionals'.

The second one. But it sounds more natural and is more polite to say: If you have hand sanitizer spray in your pharmacy, could I please have one?

*have (present tense). ‘Had’ is the past tense, so means you did have hand sanitiser, but you don’t have hand it now; so the question wouldn’t make sense as the person asking already knows the other person doesn’t have the sanitiser. Unless you are using the conditional tense: ‘if you had hand sanitiser, would you give it to me?’ (a rhetorical, not a real question).

*have (present tense). ‘Had’ is the past tense, so means you did have hand sanitiser, but you don’t have hand it now; so the question wouldn’t make sense as the person asking already knows the other person doesn’t have the sanitiser. Unless you are using the conditional tense: ‘if you had hand sanitiser, would you give it to me?’ (a rhetorical, not a real question).