I do agree that some kind of indication on how much charge is left. considering that game is turnbased, with completely various amount of things able to happen every turn (reload for 4.0s in turn or shoot in 0.2s at the same one turn). In Doom it was more intuitive, as you could do only so much in that certain time, so you had some sort of feeling how long it gonna last after few uses of powerup.
If exact counter way too out-of-place for the developers, which kinda understandable. I would suggest adding some sort of partial indication - like short bars made of ASCII characters, that dont show exact number, but how much left (full, half, low or such), otherwise - make it visible in "@" character screen as status (like adding "Fully protected", "Not too long till vulnerable", "Will be vulnerable again in a moments" or whatever sounds good for such)
Or add messages for it in event log, prefably coloured, probably the "half-spent" message for powerups would be good (except for berserk probably) unless other powerups add up too, as it various powerups vary in length in different situations.
If everything of thouse fails i would like the curent mark of powerups not just go darker, but actualy, flash between light and dark. Yes, only thouse three little letters in corner, not whole screen, i think that would attract player's attention to fact of runnin of thing just enough.