He says that HaShem wants us to say the reasons. This, he explains, comes with implicit protection from those who will try to prevent us from performing the mitzwoth be they internal (yetzer hara) or external. (idolators) How is this a means of protection? If the reasons were written down, a crafty adversary would come up with a seemingly reasonable proof for why we shouldn't do mitzwoth, and since we couldn't disprove it, we wouldn't have any defense. Instead, since we say the reasons, if an opponent shoots down a reason, we can always offer up another.
It seems to me that part of the undercurrent of the Noam Elimelech's words revolves around the obvious reality that we are supposed to perform the mitzwoth, reasons as they are might get in the way of observance of the mitzwoth. By not stating the reasons, they are changed from a weakness to a strength: We are encouraged to come up with any reasons that allow us to continue performing the mitzwoth, because that is who we are, that is what we were created to do. (Of course, this is just another 'reason,' feel free to shoot it down and we will come up with something else :) )
HaShem wants us to come up with the reasons. The mitzwoth are our pursuit of HaShem. Through them we cleave to Him and aspire to make ourselves similar to Him. In seeking out the reasons we will come to perform these mitzwoth more intimately, in the hope to strike some connection. L'havdil, we see in television shows how detectives and others seeking out a person will visit their haunts, sit in their chairs, put themselves into the persona of their prey. Similarly, but on a much more basic (and at the same time higher) level, seeking out the reasons, we will go through the motions of the mitzwoth, in order to connect with the rationale behind these (perhaps seemingly random) actions.