When I am building packages on Gentoo. I get this warning that '-ggdb3' flag can 'break packages.
I have yet to find an instance of when that is true. Although I once found some code which broke under different optimisation settings, that's different from including debugging symbols.
Could some provide an example of code which would compile without debugging symbols and not compile (or go wrong in some other way at runtime) with them?
In the "old days" I built an entire Linux from Scratch system leaving debugging on for every single binary. Sure, the install was significantly larger, memory usage was less than ideal, but I never had any problems at all, either in compilation or subsequent execution.
It is hard to prove a negative, and one can't through anecdote, but a year of running this as a second desktop/toy server would lead me to conclude that it is really not a problem.
I think the flag you are getting is the standard warning that a package will give in Gentoo if you set USE flags with which it was not tested, or with which it is not really meant to be installed. As long as you know what the flag is---and in this case, you seem to---and you are not placing it in any "mission critical" setting (i.e., you will get blamed if something goes wrong) seems safe to ignore those warnings.