Will pruning the blossoms/fruit now lead to a stronger plant and better yield in the future?

In general, yes. That is true for most all plants. Young plants just transplanted, need to devote their energy to developing roots, not blooms and fruits.

Dave

Minami, Since you are in zone 10, the shishito may end up being perennial, in which case looking to the long term, rather than short term may be wise. Also, with many pepper plants, judicious pruning early on will help establish a nice thick central stalk that will be able to support fruit later on. I currently have a manzano rocoto pepper plant that I wish I had pruned more aggressively early this spring.

Thanks everyone! One last question, if I prune aggressively now, will they resume blooming this season or will I have to wait for it next year?