A lot is determined on what kind of water you'll fish in and how high the bow rises in rough water. The numbers MK uses to figure shaft length are good and the MSRP difference between the two lengths is only $30. If you are worried about it, get the longer shaft and try the motor in the conditions you fish in. A repair shop can always shorten it and you could even do it yourself. It's not that hard.
The only disadvantage to having the longer shaft is that it might possibly take up valuable deck space on the bow when not deployed. There is no other down side. I have the longer shaft on my Riptide and there have been a couple of times I was glad I had it.
The shaft on a footcontrolled can be replaced, but not cut down. However, when you replace a 52 with the 42, the mount for the 52 is too long for the 42" shaft and will not allow the motor to ride in the correct position on the motor rest.
The 42/45" is the most common and considered "standard" for MinnKota trolling motors on most bassboats. Some, and depending on waters fished, set "bowhigh" and need the 52".