If you haven't replaced your stock dowpipes with the Akrapovic Catless downpipes (or anyone elses) then you won't even throw a check engine light.
The 1M has two sets of cats in the stock exhaust system, Akrapovic has confirmed that removal of the secondary set (in the mid pipes) will not trigger a check engine light, only removal of the primary cats in the downpipes will result in a check engine light.
The check engine light will only come on once you replace the stock downpipes with catless downpipes. If you are doing this you will need a tune to get rid of the check engine light.
In regard to your original question, if your car is fitted with catless downpipes and the ESS tune, you will have to flash your car back to stock using the ESS handheld switcher before you go into the dealer for a service (this is so the dealer does not find out you are running an aftermarket tune(ESS)). Once you do this the check engine light will reappear. Once this happens there is no alternative other than to tell your service adviser/mechanic that the car has catless downpipes and that is the reason why the check engine light is illuminated.
The way I look at it is that flashing the car back to stock before a dealership visit, thereby causing the check engine light to illuminate because of the catless downpipes and being upfront and honest about this will not be as bad as leaving the tune enabled so that the check engine light does not come on and the dealer finding out you are running an aftermarket tune as a result.
It really comes down to the lesser of two evils. I hope this answers your question and sheds some light on the situation as I understand it. If anyone else has anything further to add please do, similarly if I am mistaken with anything I said please let me know. Hopefully ESS can chime in and confirm my position.