1. Can I still change alignment in Wiz 5 in the same way as in earlier Wizardries? By how I treat wandering friendly monsters?

2. If I have an Evil Ninja in my party, can I change his alignment via the above method or is he always stuck at Evil?

I am asking these questions because I am trying to figure out if a ninja is worth the hassle of dealing with mixed alignment parties.

The answer to both your questions is "yes".

The answer to your question about whether the ninja is worth the hassle of dealing with mixed alignment parties is "no".

If you happen to have a Good Ninja in one of the earlier Wizardry games (on the same platform, and assuming you're not playing a console version), you could just transfer them over to Wizardry 5; the character will be back down to level 1 with beginning stats and no spells, but will keep their alignment. (This is unlike Wizardry 3, where you have to choose a new valid alignment on transfer.) (If you have a Thief's Dagger, or are playing the Apple 2 version, it's easy to get a Ninja in the first game, but if not, it's not worth it.)

I did not think I would mind playing around to get a mixed alignment party going but it is annoying me after all. I agree with you. The ninja is not worth it.

Also, I do not have a ninja from any of the prior games but that is ok. My fighter will remain a fighter.