looks very good
I like the no lid, as it is, option especially if it is going to be in a drawer or a glass display cabinet
my concern with a framed glass top is that -the frame might cut into the view of your pens
of course a frame-less glass only lid might work -could use the hinges meant for glass (real easy to work with) or hold it to the case with decorative knurled screws (threaded inserts in your case and not mess with hinges
also adding glass (especially with the light colored leather) might cause reflections making it hard to view the pens
Sliding glass in grooves would be an option with thicker or tempered glass
Some of the old Parker cases had fixed glass panes and the back wood piece would open for placing and removing the pens
your future cases will be cheaper to make if you use pine or MDF under the leather - save that oak to make pens
what did you glue the leather with ?