Your points about a cost-plus contract have merit but aren’t applicable here because the pens weren’t developed under a contract at all. Paul Fisher of the Fisher Pen Company had started developing a pressurized pen before the space program even began (to develop a pen that could write in other orientations than on a desk), although learning of the concerns from the program gave him renewed impetus to solve the design. Fisher patented the design in 1966 after ten years of development and about $1 million in cost. Prior to the pens NASA had been purchasing special pencils at $128.89/each. The original purchase order for the pens bought 400 at $2.95/each.

The Soviet space program bought the pens in 1969, and besides the Americans they’re still used today by the Russian and Chinese space programs. You can buy one yourself for as little as $7 if you don’t care about it being refillable. On the one hand that’s a lot for a disposable pen, on the other hand that’s not terribly expensive for a pen that writes upside-down if you need that, and might not feel too bad if you’re prone to losing pens.