This is probably the biggest issue for companions using more exotic weapon and stat types. Those like Mako, Corso, Kaliyo, Kira, Elara, etc, use weapons that can be found as loot from FPs as an orange drop that can continue to be modded up the levels. Qyzen, Khem Val, SCORPIO, etc use very rare and difficult-to-come-by weapons and it does hinder their effectiveness.
Khem val is easy to gear he uses sith warrior gear and you can easily get a mod vibrosword from commendation vendor or gtn. Scorpio and Qyzen I agree with.