My own (admittedly low-level) experience with alchemists leads me to think it might be unwise to allow a single Ability Focus feat to modify all bombs. Consider that around 6-8 level, the alchemist gets the ability to lob up to 3 bombs in a single round, and also gains access to a large number of different bomb types (including sonic and force damage, two things that bypass most immunities). Improving the alchemist's ability to overcome SR and the Reflex saves to avoid splash damage actually has a disproportionate effect on their ability to sling damage and debuffs.
Granted, there are limits (they can't lob that many bombs that many times, and their defensive options are more limited than, say, a sorcerer or wizard lobbing comparable amounts of damage around). But I think a house rule of 1 Ability Focus/bomb might be wise.