Dude, it's not even a question. Bullet Seed, along with b-air and Razor Leaf, is an Ivysaur-defining move. You use it WHENEVER THE OPPORTUNITY PRESENTS ITSELF, no matter how much damage they have, unless the opportunity for a kill is stronger. To call it cheap is pointless...it's in the game, and Ivysaur often struggles against the quicker close-range fighters anyways, so he needs something good to help out at that range (there's also n-air).
But yeah, even if they're at 130% or something, continue to use it if they're close enough, because the more percent you safely rack up, the easier it will be to kill with the moderately powerful moves, like up-tilt, back-throw, up-throw, dash attack, and off-edge b-air harrassment for the gimp, such that you have a wider range of final KO options.
Like Kitamerby said, spamming the move later on is bad because you become predictable, but it's still Ivysaur's ultimate in-close punisher. Spot-dodging or air-dodging into it will usually land.