It's true that in Roman Republican times, manpower was an issue, but that was more than 1500 years before the EU3 period.
I've recently read a book on the Thirty Years War and not once was it mentioned that a ruler got into military problems because there weren't enough recruitable men available. It does mention, time and time again, about state bankrupcies, armies deserting because of late pay and other monetary issues. While it's true that the TYW did devastate Germany and of course had serious economic repurcussions, I'm not convinced that this means that state armies are restricted by the number of recruiteable men within the borders (i.e. manpower).
I would like to see evidence that during the Early Modern Period (before the Revolutionary Wars), nations got into military trouble because they lacked manpower or that extensive military recruitment let to economic problems. If it did happen, then of course I would like to see it incorporated into EU4. But to my knowledge, this whole manpower or "recruitment denies the economy its workpower" issue isn't historical plausible for most of the Early Modern Period.
I agree. The main limiting factor in wartime should be money.
There should also be some limits in terms of men existing trained for war. But, there should always be plenty of mercenaries willing to step in to fulfil the "market demand" for soldiers.