Since the label is sewn into the inside of the suit, how would anyone know that it is not there? I normally staple it into the inside of the suit so that I will remember that I have had it checked. If it is not there, you might get it confused with a different suit that you need to check.
Marit Ayin is a matter of how something appears to people walking by and seeing it. An example was the necessity to put the box of nondairy creamer with the pareve marking on the table when they first came out. Now that they are well known, that is no longer required by the hecsherim at the caterers that I have seen.
Thus, the shatnez label would not be a case of marit ayin because it is something that you would check for yourself and not need the certificate. For example, it is only at a catered affair that the cateres put out a sign saying what the hashgacha is or restaurants put up a hechser sign. You would not do that in your home.
In fact the Baltimore Star-K gives out a shatnez label but does not sew it into the suit. If you want it (for your own reasons) fine. If not, you do not need to put it in. As I said above, I just do it so that I will remember when I buy a new suit.