Stock Duke3D had a more archaic CON compiler that did not understand these issues during compilation time. Issues that were always there and always functioned like they do today.
No decision was ever done to "hide" things as far as I know, it's more that the CON engine itself was much less mature and it didn't even know when things we're broken.
EDuke32 and EDuke is all about extending the CON language, naturally it also means that catching any errors is much more important to a modder than it was before as more and more "hardcoded" behaviour is instead added to a custom language with it's own compiler.
Reporting of potential issues is provided as a form of convenience for the user, it might be ugly for first time users. However it will not change the outcome beyond complaints in logfiles or bootup.
As users will use the original code for reference undoubtedly, it opens a can of worms when trying to suddenly hide things from sight.
-> Suppress specific lines: This gives users broken code to study from as they have no idea that it's broken. While very low in risk, it's a bad practice.
-> Suppress errors for stock cons: The moment users copy and modify even a single byte of the CON, it will throw errors all of a sudden, never knowing why their single byte modification keeps breaking it.
I believe that due to above, keeping a harmless warning in a port designed primarily for modding makes the most sense, maybe their first entry-level task could be to fix the issue in the first place
Anyway...
I'm sure you can agree that the task of the CON (or any) compiler should be to follow the very spec that was outlined by the original author(s) in the 90s.
Any warnings that you encounter in 2021 would have been fixed back in the 90s extremely likely had the developers known about it.
In this specific case it's the same as pointing out that a C compiler from the 90s didn't throw you warnings about code you wrote that did wrong, undefined or potentially dangerous behaviour. But then the same version from 2021, while it still compiles your code with the same behaviour output (perhaps faster & optimized), it will throw you a warnings about the issues instead.
Coders get smarter and it might take years before someone catches an issue.
CON has a run of other bugs and undefined behaviour that devs have documented over the years, in many cases these get discovered by modders after hours or days of head bashing and thus a helpful warning gets added as some of the behaviour might not be logical at first but it just turns out that the spec is technically limited in some way. Generally warnings should still only appear for major issues but the point about us learning new things is there.
Personally I think it should have a mention in any readme / FAQ though.
A recap:
-> Errors you get in stock duke3d stuff are not cause by the gamer, they were caused by Todd.
-> CON files are part of each respective game, expansion or such. Duke3D CON files are copyrighted code. Although can be shared for mods (would eduke need to bundle CONs for all version now?)
-> Original behaviour of compiled CON is maintained regardless of the warning
-> EDuke32 does not touch original assets, i.e. see maphacks.
-> Any issues beyond these, i.e. old mods, reinforces the point of "copying from a bad reference" (remember, these are generally just visual warnings, not showstoppers).