Research points from salvaging wrecks, chance to learn component, ship, or PDC design or star system data from interrogation, theoretically Tac intel window stuff (but I don't really know what or if it ever workd properly).
As for how often it's checked, the answer is 'once per build increment (in which the officer is doing any of that stuff)' -- so, practically never, because interrogating P.o.W.s takes a few hours each, so it's over pretty quickly.
Most bonuses, for most leader categories, cap at 65%. Military leaders have some that go much higher because they're on a different scale (training, for instance) and there was at least two bugs for Naval officers that I don't know whether they have been successfully fixed or not (ISTR fighter combat didn't cap properly, and there may have been something else involved as well; the other one is that apparently Fighter Ops works backwards from how it's supposed to). As for scientists, they have a quirk that can be very aggravating for a perfectionist like me: their research bonus caps as soon as it goes over 55%, so if they hit 60% they stop there instead of going to 65%.
About 40 years in; I have a 60% DS with 60 lab max, a LG 60% with 30 labs, and a 55% CP with 30 labs. I had a few more with those high numbers but they died off in the last decade.
So, 20 years into a conventional start, I see a report that one of my officers hit 75% fighter combat bonus...
And my planetary governor is not bad with 35% shipyard, 35% factory, and 25% mining, with a small amount of wealth bonus and pop growth bonus as well. Not the best I have had, but pretty good for this early in the game.
What is the highest bonus to a scientist you have seen? 60%, 65% seem about the top I get. I think I saw a 70% once.