Would drilling holes in baffles of stock pipes on Honda vtx effect engine performance?

Yes is the short answer. You will want to change the jetting after you change the pipe the pipe manufacturer should have the specs for that. Most people claim more power and imagine there is since less restriction. That said I put the stock exhaust back on, I know I am weird but prefer the quiet over the deep throaty hog sound. I have not noticed any power loss in going back to stock.