Well, that 100% depends on if you have the governing capacity or not and what you want to do moving forward. If you want to keep expanding in trade company regions and have spare gov cap, you can state parts of west africa and the maghreb, its easy enough to get the merchants their with only a few territories and the loss of trade power doesnt really hurt. If you want to keep going and dunno conquer all of western europe, you might wanna keep a bit of room for that.
Otherwise, if you meant with "...keep extra provinces out of the trade company..." to make them into territories-no. No need. TP-provinces do not have a built in malus to manpower compared to territories&if you have expansion ideas, you can also build the investement that gives you manpower (Dharma DLC), it would be the same as having a 20% manpower boost in the entire area.
Since money is no longer a factor for you at this point so you can afford to build as many townhalls as you can-a trade company province with a townhall costs you 0 gov cap, so that is also not a problem.