You are right; it is not illegal to edit Gerbers, but the intent is what is wrong with your action. Sure you can modify and hack it, but the principle of the matter is that you are trying to circumvent one of the limitations of the software to avoid paying $49.00 and not really rewarding the person that put the effort into it.
You got that wrong.
The PCB layout i create is
MY work,
MY intellectual property,
I am the copyright owner of that work.
The software placing a label on the PCB does not change that fact in any way.
On the other hand, the copyright of the DEX software code and DEX' own file formats is owned by of Iliya or his company (i guess). So Iliya has the final say what can and cannot be done with his software and with information stored in his file formats.
The copyright on the Gerber file format is not owned by Iliya. Neither owns Iliya the copyright on the PCB layout i create in the software. Furthermore, the Gerber file format is an open standard. Who are you to say what i can do or not do with my own PCB layouts stored in Gerber?
Being the copyright owner of the DEX software, Ilya could demand as part of the licensing terms that the copyright on any work created in DEX is owned by him. Let's just assume that such licensing terms would be legal in your jurisdiction. By using the software you would agree to those terms and then Iliya could decide what to do or not to do with the PCB layouts you created. But even if it is legal to put such terms, it would be a stupid and suicidal move to do so...
You could also argue, that the label placed by the free version is a reminder, and by making it inconvenient for you to remove it makes the free version of DEX (slightly) less comfortable/elegant/whatever than the paid-for version -- which is actually the original intention of the label in the first place -- separate the free version from the commercial version.
Why it should be wrong to remove the label in my own Gerber files i do not understand.
What is the benefit of the label being on the PCB layouts, aside from it being a reminder and a feature that distinguishes the free version from the paid-for version (without being it a major annoyance or restriction for most if not all practical purposes)?
Will the possibility of editing Gerbers have a significant negative impact on sales? If you have to answer with yes, you have a problem with how you position the software in the market and you need to rethink your product and/or sales strategy...
It is probably for the best to adopt a 'laissez faire' attitude with regard to this matter.
After all, when people do this it also means that they are
users of the software. They might or might not turn into paying customers in the future. But they are part of the user base. By hopefully sharing/publishing their projects made with the software, they help raising awareness about the software, which could lead to other people purchasing it. Chastising these users will probably only keep your user base smaller than necessary. And a small user base is only viable and paying your living costs if you have reasonably high margins on your software sales... Well, personally i believe not that many people will bother with the additional step of removing the label from the Gerber files anyway...
<EDIT: Corrected backwards sentences that came out in the wrong way...>