I count 245 pilots, and 259 upgrades. Trying to price each pilot + upgrade combination would be 58,555 combinations to work through. The actual number is less because not all ships can take all upgrades, but it's still ten thousand or tens of thousands of permutations. Trying to implement any 'combination taxes' for permutations of particular upgrades, with particular pilots, gets into the millions of combinations.
Simpler is better!