A properly assembled square taper bottom bracket should be trouble free for years and years. I don't notice any difference between square taper and external bearing BBs while riding, but I believe there might be a difference if an engineer calculated the stresses and deflections.

Something that can make a big difference is chainring quality - shifting on a set of FSA rings is significantly inferior to that on Shimano rings. that alone could be worth the trouble for the upgrade - new Shimano rings to fit the FSA crank will probably cost similar to a Claris crank & BB.