Without knowing the intended end appearance, it is impossible to tell ...
but my gut says to mount the hardware AFTER all refinishing steps have been
taken. This eliminates the hassle of avoiding the hardware while applying
the finish. If you want to darken the finish near handles & such, well, you
have the mounting holes to tell you where they go ... use those as
approximate guidelines to apply somewhat darker stain near them. If you want
an even coloration, by all means leave the hardware off for now ... having
to work around it will prevent even application of stains and finishes.
Make matters as simple for yourself as you possibly can. There will be
complications enough in actually applying the finish.