I was going to come in here and ask how such a blatantly obvious question which requires a "Yes" answer had gone three pages. But I see where the road bump is now.
I think the answers are being made are mostly all good...but perhaps a bit unnecessary from a RAW and RAI perspective.
Simply put...what is a magical bow FOR if it doesn't imbue its ammunition fired from it with its properties (say, for example, +1 to hit and +1 damage)? Is the receiver of the wonderful magical item, presumably a decent (if not primarily an) archer, expected to run up to foes and BEAT them with their +1 bow to get their benefits?
No. You are supposed to fire arrows out of it. So your arrows are +1 to hit and +1 to damage. IF you want to split hairs and say "But what is that +1 for/from? HOW does it happen? WHY is the arrow now magic?" The answer, as it has been since dice rolls immemorial, is...
"mmmmmMAGIC!" <jazz hands>
If we start down the road to explaining "what/why/how" MAGIC happens, then you are firmly marching into "Magic=Science and therefore HAS an answer that must be discernable."
If you prefer a bit more rationale/detail in your world, the answer is still simple: "It's magic. It works because that is the nature of the enchantments placed on the bow. It transfers some of its magic/"energy" into its ammunition and that "energy" makes the ammunition capable of bypassing a creature's non-magic weapon resistance."
If you want to say it tranfers +1 to hit but only gets +1 to damage if the creature is hit by non-magic weapons...then the magic /is/[potentially] effecting the damage...after the fact [being hit?]. Sooooo...in what way is the arrow NOT magical if it's getting a bonus to damage "maybe"?
The whole thing is a black hole of logic or justification. It's magic. Yes it works. It works BECAUSE it's magic!
Moving on.<jazz hands>