>>They are approx 50"x20"x14" I'm thinking of building a frame type rack and using these tubs with the tops still on.
What do you mean by a frame-type rack? Do you mean a rack where the box will slide in a track of sorts?
If so, that is not a good idea for a few reasons. I won't get into that in case you meant something else.
If you just mean a glorified shelving system to hold these boxes, I think that will work fine.
>>There is a chance future tubs may be translucent green or even opaque. What I would like to do is cut a large window on one side. Take a piece of clear acrylic and silicone it over the hole - maybe have an inch overlap. It would be even cooler if a rail could be mounted to allow the acrylic to be a sliding door. The one drawback is the the cage is ribbed and may have to fill gaps to get a proper mounting. Maybe a foam bead around the window area. Do you think it will comprise the structure too much?
If you just want to cut a large rectangle out of the box and attach a piece of acrylic, this will not effect the structural integrity of the box too much. I have seen this box and the ridges will pose a problem, but they can be dealt with.
Regarding the sliding door idea, this will also work but you'll need to attach a frame of some sort to support the sliding track. It would not be difficult to make a wooden frame and attach it to the boxes. I do something similar with 50 gallon storage totes but in my case I attach them to the opening of the box as in the pictures below.


You're talking about something different with the frame being attached to the side, but a frame like the one above attached to the side will offer sufficient support for a sliding door system.
My only other suggestions will depend on what you mean by the frame style rack.
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Current snakes:
1.1 Gonyosoma oxycephala - (Silver/Yellow)
2.2 Gonyosoma oxycephala - (Green)
4.3 Gonyosoma janseni - (Black)