Bitmain definitely knows what they're doing & if someone can optimize anything on that board - it's them. They're not obliged to tell you anything & can use whatever software/hardware they want, & then you can do what you want with it.

That aside, there's a lot of info/documentation on their asic chips lately. Tons of folks are soldering them to their own PCB's. We're already seeing many projects with one or two asics on small pcb's controlled by some small mcu or via serial by a pc, next they're going to put 5 on a board, next 10, then you're going to have full fledged open source s19 type machines. It won't change anything though - The vast majority of the cost of a sha256d miner is in the asic development/wafer printing - even if you hand crafted a shad256d miner asic by asic, resistor by resistor, etc, custom controller board, etc with your own soldering iron - the cost would be similar to MSRP for a s19, for example. Bitmain is selling those machines for very, very close to their production cost. Just in case you're thinking it's cheaper to build your own miners.

To answer your question though, how much to hack a fan control? That's more of a reverse engineering job than development, reversing costs are generally much cheaper than programming. I'd say not as much as you'd think, plenty of forums with lots of talented reversers who'd probably work with you for a few thousand US. If you want a custom pcb controller board with tested, quality software, you'd need to start adding 0's to the price.