This is not a reptile-specific answer, but in general there are good reasons to avoid using antibiotics until they are really necessary, in humans as well as in animals. One reason is that antibiotics can have an impact on the various assorted beneficial bacteria that are involved in digestion (and all sorts of other bodily processes that we don't necessarily even know about yet, but digestion is a big one).
The other reason is that every use of antibiotics increases the chances that more of the bacteria will become resistant. Antibiotic resistance is a major issue on a global public health scale when diseases mutate so that the drugs used to treat them stop working in whole populations; and also on an individual scale when someone has a persistent or recurring infection that stops responding to treatment after awhile. Ever hear of someone with a horrific un-treatable flesh-eating infection? That's a victim of antibiotic resistance.
Basically, what you really don't want is to treat the scale rot with antibiotics, but a handful of germs manage to hang around somewhere that weren't killed off by that round, and then reinfect the snake later. Do that a couple of times, and you've basically selectively bread a super-bug of a scale rot infection that doesn't respond to available drugs. Or that no longer responds to the safest drugs, and you have to resort to the ones with nastier side effects.
Basically, if you want antibiotics to be effective when you really need them, don't use them unless you really have to.
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