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I'm working on a apothecary cabinet for LOL and have the option of staining some parts before glueing. I like that option since it eliminates the problem of glue stains.
However, my question is does a piece of stained wood interfere with the chemical action (bonding) of the glue making it less strong?
Jerry,
It will interfere with the bond, but don't fret. Take some blue masking tape and tape off the surfaces to be glued. For mortices, stuff some paper into the them prior to staining. Afterwards, remove the tape and paper and glue away.
For an apothecary cabinet I'm guessing dado's, rabbets, and maybe half lap joints are what make up the joinery? If possible, stain the wood before you cut the joinery. That way you'll get bare wood at all the glue joints. Otherwise, do the masking that Maurice mentioned.