The different lengths of shocks will give different heights to the saddle.
What I did with my build, was to use a length of bar, with holes in it. One end bolted to the swing arm, the other end drilled at 190, 200, 210,220mm and then tried each position to see what felt comfortable. For me it was 200mm. Any longer and saddle height was a problem.
In shocks I have tried 190mm (which I had) and am now using a 205mm motor cycle type (Being I am heavy and needed the stronger springing).
The 205 shock I have, while only 5mm longer than my ideal, just makes the bike a little high with the saddle fully down.
As for difference in travel and performance, I never noticed any difference.
My bike is used on road all the time.
So, my suggestion, is find out what is the right height to suit you and then look for shocks around that size and unless you are using an air shock, you will need to find out what is a suitable spring strength to suit also.