If you are thinking about doing it, I say go for it. The intake needs to be out to have the work done, now seems like the best time to do that. I dont think I have ever heard of anyone taking one off and the boat running faster. They could have the shoe shimmed too low and that could create drag. Just takes an adjustment to fix that.
Generally speaking, I think 70 mph is a good point to install the shoe/rideplate. Others may disagree. All depends on what your goals are with the hull. If you want to go fast, do some research and find out if anyone has gone fast with your hull. If not, then it may not be the best candidate and in that case I would not waste a bunch of money trying to make it go fast. If it has potential and you want to go fast, then by all means do it now and save yourself the trouble of yanking the motor,pump and intake later on.