Personally I can't say it ever really bothered me, if I was looking for something specific I would just pick it up in decent condition regardless of punch.
I think an unpunched Kenner looks "neater" and of course could suggest that it hadn't been pushed onto a peg in a store but it's not a deal breaker for me.
Trilogos are rather interesting actually because a lot of cards were factory punched so anyone looking for strictly unpunched cards thinking that is a more mint example might well be passing up nicer factory punched cards thinking its a flaw!