I am looking into replacing my Ultegra 53/39 with an FSA 50/34. For this I will need to change out the BB as well. The Ultegra BB is 109.5mm and the FSA BB is only available in 108, 113, and 118mm sizes. Does it make a difference if the new one is slightly longer/shorter?

It only makes a different specific to the crank, too long or short and it will screw up the chainline. For the compact FSA it should be 108mm width spindle, as most double cranks are right around this range. The 113 should be for mountain bikes, 118 for triple cranks. If you still have any doubts, check the info for it in almost any online shop, it should list the bb spindle length (now you just have to know if you need 68mm threading or 73mm (68 being by far the most common in my experience)).

No, but yours is most likely 108mm anyway.

Spindle length depends on the crankset, not the frame. Check the specs for the crank - I'm pretty sure the FSA ISIS cranks use a 108mm spindle. If two sizes are listed, typically this suggests that you use the smaller size on bikes with skinny seat tubes, and the larger size with fat seat tubes, since fat seat tubes will tend to push the derailleur further out.

I have an FSA Energy 50/34 crank octalink. It bolted right up to my 109.5 Utegra bottom bracket so the only thing that I had to buy was the crankset.