Its pretty easy to hit the cap in a game you are playing for max points. I dont recall the exacts, but its like 40 something colonies and 255 units. Anyway, to your question, I am not aware of any method of removing it. And much to our mutual loss, ColFans is dead.
I vaguely remember the unit limit now (I haven't played the game for long time). It's probably more like 1024 units though (255 would be way too few), although one should check the exact number. As for the colonies, I've never had this problem. As mentioned above, Colonization is a very different game from Civilization despite the looks, and there are no benefits to Civilization-style expansion. It is better to have two colonists working in one colony than each founding his own colony, if they are going to produce the same resources. I typically win with 10-12 large colonies with maybe 1-3 additional resource colonies in the hinterland, so I don't see how one can reach 40 unless playing for the lols. The logistics of it and the amount of micromanagement will kill all fun.
Its 255 (or so) on the map. Colonists and such inside a colony dont count. The colony limit is based on the European powers. Again, I dont recall exactly, but you have to take them over to get additional colony count, that kind of thing.
Now, to the ancillary statements because any conversation about this game makes me happy... Two colonies with one colonist is unquestionably better than a single colony with one colonist, simply due to the base square not needing a colonist to produce resources and the base colony production of liberty bells. So even if the colonist is needed to produce food, the base resource of the colony tile always provides more than a single. In fact, generally speaking you should use your first two colonists to drop two colonies immediately. Extrapolating a bit further, as you grow it is also allows you to avoid the Tory penalty longer as you have more spots for more colonists. You are correct that you dont "need" a Civ like expansion, but it is certainly possible and has value if you choose to do so. And frankly, required if you expect to get a max score on Viceroy.
Now, this does assume that you are playing with a goal in mind other then simply winning the War of Independence. A perfectly noble goal and a wonderful choice for many players. I am sure you have noticed, and seemingly already have done so, winning that war is relatively easy on all levels. Almost impossible not to without ignoring aspects of the game (which has merit as well, like eschewing European trade, etc). I believe there is a thread on this forum for game variants in fact.
Additional data, if not an actual answer... https://www.gog.com/forum/colonization_sid_meiers/255_units_and_other_limitations