Umm, just used the golden whetstone on the bow. I probably should have guessed, but that just wasted the whetstone instead of adding damage to the used arrows... might want to restrict the whetstones to weapons that they can benefit (I don't remember all of them at this time, but bows, in particular, don't seem to themselves do any damage, so most probably could do with not working on bows...)
In previous versions, bow's were tricky to figure out total damage. A jewel or stone would indicate on the bow that it would do extra damage, and it would, but selecting/activating the bow and then highlighting an arrow would not indicate the total damage. You'd have to count the enemy's health and watch for the "double attack" numbers. It might still be doing that?
Or maybe a plain bow with zero additional damage would still really do zero times 1.25 = zero additional damage. Definitely needs clarification.
A bug related to the "double attack" was, IIRC, using an arrow would make you get hurt by spikes TWICE. If anything, arrows should be immune to spikes, they're a long distance weapon after all...