Multimedia timers just takes a little bit more of your ressources, it doesn't mean mIRC's CPU usage will spike quite a bit, it might if you are using a very small millisecond delay and the associated timer command is doing something heavy, but that wouldn't be your case here.
Something that could be a problem is that it can prevent Windows from going into sleep mode.
You are stuck because you don't want to use /timer -h and count the time that way because it's innacurate and you are right (if each new timer triggers one millisecond later, after 1000 timer you are off by one second) and you don't want to use the TIME parameter of /timer because of the system clock issue.
