The only thing that would effect the WO noticeably would be the sheet of plexiglass.  If it is to thin it will flex and make weird noises, and it won't make the subs do what they are supposed to, basically flexing = bad.

With that said, I would recommend plexi thicker than 1/2 inch.  the thickest you can get the better though.  

But yeah, painting and lighting shouldn't effect the design to a noticeable degree.

I have not tried lexan, but I did use plexi less than half an inch and it flexxed like mad, so much so that I destroyed the box after removing my subs.

I did make one WO that had windows in it though.  I doubled up 3/8 inch plexi sheets and made 4 windows, for the two outer sides of the sealed chamber.  Than I mounted the subs facing the windows. It looked really cool, except my plexiglasses work at the time was horrible.  

On that same topic, another route would be to go with several windows rather than a single large sheet.  And you can glue plexi glass together.  CLEAN IT VERY WELL.  Than use plexi glass glue. (I got it from a place downtown)  It actually chemically bonds the plexi.  If you get good coverage (MY glue seeped out the edges)  you can't tell its 2 sheets.  I practiced on several small pieces before attempting the larger pieces for the windows.

Think of panel vibration as sucking energy out of your sub and creating distortion with it.

Then decide at your own risk how much you are prepared to deal with.  I have a box made of 2 inch thick solid doors and it still flexes.  The thicker the better.  The least area between connecting panels, the better.  The more bracing the better.

Real glass is better (heavier and stronger) but is harder to permanently attach.  If you don't need it permanently attached, just run weatherstripping or similar along all contacting panels and set it on top (but it has to be good and heavy and perfectly sealed).

It is impossible to get rid of all vibrations but doing what you can to at least try will go a long way.