Does your vacuforming machine recommend a thickness? I would estimate the starting thickness your stock plastic to be reduced by half when the material is stretched around the form (assuming the surface area doubles) So 0.010" stock would be approximately 0.005" thick when formed. So for this example in 1:32nd scale the stock 0.010" plastic is 0.32" thick in scale thick and being reduced to approximately 0.16" scale thickness after being stretched. According to their website Evergreen makes clear polystyrene in 0.005, 0.010, and 0.015" thicknesses.
Unless someone is aware of a reference with some 'non-standard' aircraft dimension specifications you're going have to take a guess at the canopy thickness. Based off engineering judgement I would make these generalizations: Windscreens and forward facing glass are probably thicker than side and rear facing windows, pressurized cabins are thicker than non-pressurized. I'd guess most folks do like me and make it thin (>0.010) so it doesn't look ridiculously thick like some of the older kit canopys.
Squadron Thermaform has not been available other than Ebay for years. It's good stuff with the advantages of not needing a vacuform machine all the waste of using an entire sheet for one small mold that comes from using a vacuform machine. Near as I can tell Squadron has gotten out of the 'stock' plastic business as it not even a category on their website. Spruebothers sells Evergreen.