Translation:Excuse me, sir, what time does the bus leave?
You can use either. The more compact "perdón" is a common interjection that means "sorry," "excuse me" or "pardon me." If you say "perdone" you are using the verb in the imperative mood. It's a little more formal to use "perdone," since that corresponds to the "usted" form of "perdonar."
That's mostly correct, but the more usual/common translation of "hora " in this case would be "time."
Normally, "hora " translates to "hour" when forming time expressions (e.g., "the movie is three hours long" = "la película es tres horas de duración"). It also translates to "hour" in various colloquial or idiomatic phrases like "happy hour," "office hours," etc. Otherwise, you should think "time."
Couldn't you say "what time will the bus leave?" I know you have to say "va a salir" for that translation. But colloquially, if you're asking "a que hora sale el autobus" you assume the bus hasn't left. In english, I've heard people say "what time does the bus leave?" and "what time will the bus leave?" pretty interchangeably assuming the bus is yet to leave.
I think you answered your own question. Yes, those are pretty interchangeable with this question. However, both of those English expressions have parallel constructions in Spanish. So, I think the issue comes down to whether a native Spanish speaker would use the simple present where a native English speaker would use the future. I'm no authority, but I'd say no. I think present and future tenses are commonly used in both languages in this context. I don't have any reason to suppose native Spanish speakers routinely use the present tense while native English speakers would use the future tense to ask this question.
I will add that a native English speaker could also ask "what time is the bus leaving?" and that would not be expressed using the present progressive in Spanish. Most likely, that would be asked using the simple present tense, but a "going to" (i.e., "va a salir") future tense would also work.