Well, I've yet to see any code released that isn't considered to be "beta", so I'd say "debugging" is relevant at all times. When users give you vague reports of getting errors without being able to tell you where that error occurred, you'll wish you'd left it as lineNumbers.
The question, however, is what is the cost of that line-numbers information? Well, I imagine it would cost a trivial amount of extra CPU cycles to generate it, and anyway, you usually compile functions once at the start of a mission, so that extra time is pretty irrelevant (in-game FPS is what matters, not FPS at startup). The relevant side, however, is that the game will store a complete copy of all function code (well, comments will all be trimmed by the preprocessor) . However, even the most complex script suites would barely waste any memory (e.g. all the scripts I've written would not amount to more than a couple of megabytes) and would probably just get swapped out to disk anyway, since the stored copy of the script isn't actually used, except when errors occur.
Perhaps I overstated my original comment though. If you don't want to use preprocessFileLineNumbers because you think it might impact on the performance of the game (I personally don't think this will be significant), then that is fine, but most people seem to use preprocessFile because they want to avoid typing such a long command (and virtually noone knows what the lineNumbers feature actually does!).