That's interesting. But the issue with that now is that once you have a bomb pulled out, you only have specific options you can use. I'd be very surprised if a Bowser player still attempted to commit to an attack like that with a bomb in your hand.
That's not to say that UpSmash is bad in that situation, but it just sounds like lack of awareness on the part of your opponent if that seems to be working very often lol
But yes, as a general tip you usually don't want to attack Bowser when he's directly below you or he has his shield up, so using a bomb, if you really have no other way to escape the disadvantageous position, or if you have to just get rid of it anyway, isn't a bad idea. If bowser is shielding, try to use moves that recovery quickly or require minimal commitment (jabs, spaced aerials, etc) to try and bait a bad whirling fortress from the Bowser or some whacky reaction to your pressure.
edit: I totally just assumed you were talking about that from Link's perspective, but now I'm extremely confused.