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Can you glue two painted pieces of a model together, even if there is paint on the spot where you need to glue ?? Would it affect the strength of the join?

Depends on the glue. With superglue you can, but it'll be easier to snap.

You can do this but are relying on multiple weak adhesions;

plastic<paint>superglue<paint>plastic

Super glue will hold the paint fine but it will more likey pull the paint off the model. Which is fine as you can glue it again but it will almost certainly disrupt the surrounding area.

May advice is to scrap the paint from the surfaces that are to be bonded and then glue. A little work up front will prevent or at least minimise problems in the future.

Plastic glue should work fine, since it just melts the plastic together. The only problem is if you want to be able to keep the paint on the glued part

I've done this before, it works just fine. But the join is weaker.
Recently I threw a batch of Space Marines into the dettol soup to strip the paint. I soon remembered the joins i had painted before gluing! The paint under the glue loosened and lets just say I've got some building to do!
I don't mind however, This is an opportunity to install magnets and whatnot
Untill now I've not had much issue with the bond being too weak for general usage though. If you want the best possible bond (I guess you should) then use a file or a hobby knife to carefully clean a bit that will contact without wrecking your work

For plastic glue, I scrape anything more than a light dusting of overspray, which will melt without noticeably weakening the bond. For superglue, I make sure to keep surfaces completely free of paint, usually by masking with poster tack before priming, then leaving it in place until assembly.