I think it depends a lot on where you're starting from. As you say, a longer fork will raise the bars, and also tilt them back towards you very slightly, but you can usually put it back how it was by changing the stem/bars to ones with less rise (if you want to). Whether the change to the head angle is good or bad depends on what you want from the bike. A shallower head angle will improve handling on rough sections, but won't be a benefit if you don't need to improve the handling on rough sections.
Raising the bottom bracket is generally a bad thing, I think, based on the advice I've read that says to have the lowest bottom bracket possible for the style of riding you're doing. (A higher bottom bracket raises your centre of gravity, and handling is improved by keeping your centre of gravity as low as possible.)
Longer forks would also make the seat tube angle shallower, which is a bad thing if you want to ride up hills.
It depends on how big the difference is, though. If you like the way your bike is set up, it makes sense to keep the fork length as close as possible to the original.