Genrally, the size of the biggest Merc units grew between 3050 and 3067. Multi-regiment commands became more common, and smaller commands would often go up a step or add more supporting elements to them. They then crash hard during the Jihad, to the point where there's only a single multi-regiment command left in its immediate aftermath. Between the general peace of the Republic era and the RotS' actively putting the brakes on the merc trade, they don't really recover until after Grey Monday. Even then, by 3145, unit sizes are still small; a combined-arms batallion or less is the norm, and there are still only a couple of multi-regiment commands.
Note that this is just from the units listed in various Field Manauls and the like. Those in turn represent just a tiny portion of the Merc trade and, even then, more of the top end of it. For the 'average' unit their size probably remains reltively constant throughout.
