Usually with mods it doesn't lag, as the largest mods tend to only change the entirety of the game, which only makes it lag as much as the game did originally.
But if they have more content than the original game, than yes they would lag more.
Yeah. Mods that add a lot to the base game would probably add more strain than a Total Conversion, although my game usually is a bit more sluggish with some TCs. With vanilla I run the highest settings and it runs like a hot knife through butter for the first few hundred years. In my longest game ATM, I'm over 400 years in and I think the reason why it's so much slower is because there's been a population explosion. Pretty big every king/emperor's dynasty has hundreds of living members(and thousands of dead ones, but I don't think that affects performance). The devs also said that castration, blindness and some Muslim decisions are optimised really poorly and are constantly checked by the game engine. Usually the Muslim blobs and Byzantium stay really big and since CK2's population always explodes, there's thousands of characters constantly checking the same decisions which puts a huge strain on the game. In the next patch the devs are fixing those among other things so the game would run much better, but they really need to fix how the numbers of characters multiplies so much. It's unrealistic and it's a major cause for late game sluggishness.
Anyway, so that this post isn't completely off topic, here's my game:
I started as the Duke of Wessex in 769. Up until 1000, I tried to expand slowly so I wouldn't be a megablob. But then I got bored and I went from England, Scotland, Wales and Saxony to my current giant empire in less than 150 years. My dynasty leads every single Holy Order but they all convert to random cultures as soon as they become the leaders(because Holy Orders have hardcoded cultures for whatever reason).
The Shias managed to crush the Abbasids(who are now a tiny Shia duchy) but then they collapsed into several countries. The light green duchy of Algers is the last Sunni realm. The light yellow in northern Spain is the Yazidi Empire of Hispania. Formerly the Sunni Umayyad blob, with all of North Africa, Spain and Aquitaine under their control, they are now a tiny Yazidi state ruled by house Sanjo(who are just about to be overthrown by rebels.
Ethiopia is divided between two Ethiopian Monophysite countries. It's a miracle that they managed such a huge comeback. A Monophysite ruler originally united Ethiopia hundreds of years ago but after Muslim invasions and tons of rebellions, his realm(although it was a descendent ruling by this point) collapsed. Ethiopia was divided into lots of Muslim emirates(the Abbasids being one) and a few Ethiopian duchies but somehow they prevailed and reunited. The Abbasids had created the custom kingdom of Nobatia, which is now the lighter of the Ethiopian countries(although it's no longer Abbasid or Muslim). The Abbasids managed to pop up again as a small duchy just south of Armenia. Mali is still West African Pagan and they managed to expand into North Africa even before the Byzzies and I weakened the nations there.
In Eastern Europe, the Slovensky dynasty rules Bohemia, Poland and my vassal Lithuania. They used to rule Russia and Ruthenia as well back when they were pagan, but when I converted both of them to Catholicism, rebellions caused them to collapse into tons of minor states. Several nations such as Byzantium, Finland(who were once a huge Estonian Suomenusko blob before the Norse king of Sweden inherited somehow. It was reborn through gavelking as a weak Norse state), and even Poland took slices of Russia and Ruthenia. Up until 1050, pretty much every Eastern European country was still Pagan but now only Poland and some minor OPMs are Pagan.