The process used by the miltary is somewhat more complex than just painting the canopies. I'm stealing this from the AMARC Expericence site at:
http://www.amarcexperience.com/AMARCProcesses.asp. He explains it very clearly:
"Seal Aerospace Vehicle for Storage
Most of the aircraft at AMARC are protected by a vinyl compound called Spraylat which is sprayed on as two coats. The first coat is black in colour and seals the aircraft to protect its systems from dust, moisture, animals and insects. The second coat, which is white in colour, helps to reflect sunlight and heat to protect the aircraft from excessive internal temperatures. Before the spraylat is applied the engine intake and exhaust areas have desiccant material installed into them, and other openings are filled with barrier material of barrier tape. All access panels, doors, plates and other small openings are sealed using tapes. Brushable spraylat is used in conjunction with the barrier materials and tape to ensure a complete seal. Cockpits are vented and glass and acrylic surfaces are cleaned before the spraylat is applied to them."
In the museum we compromise between effectiveness and attractiveness but we have to do something. If you don't the canopies eventually turn yellow and look far worse than any coat of paint ever could. Those museums that haven't done it are eventually going to regret it when they go looking to have a new canopy made for their F-15 to replace the one that looks like it has cataracts.
James