It's probable that saving is somehow causing the game to freeze this way; there are a LOT more of things to save in LI than vanilla, the core of these being the metric ton of buildings we have, but of course also counting character/provincial/global flags (SELIN applies provincial flags IIRC for every province in-game, and that's a lot of flags), characters and whatnot. This causes the game to allocate a lot of memory in creating the save file and well... no doubt the freezes are due to memory shortages the game is having (independently of how much memory you allocate to VA). The only solution I can think of is reducing or simplifying our buildings techtree... but that's one of the core design philosophies of LI and a lot of work has gone into it, so we have to be careful when treading around there. That's Riknap area of expertise anyway, so I'm counting on his opinion here.
EDIT: I've been running tests the whole morning on this. I've reverted buildings to vanilla, disabled all custom portraits and their sprites and reverted some interface province files to vanilla and I still get freezes on clicking holdings while
the game is unpaused. This seems to be the thing, the holdings are freezing the game only if it isn't paused, when paused, I clicked on at least 40 different holdings without a single crash. Clicking while running results in only 10 holdings before getting a freeze.
It's indeed also happening during/after autosaves, I don't really know what the problem is at this point. As I said before... we should either wait for those memory fixes paradox has promised or start debugging the mod one section at a time to better analyse the problem.
Further testing: I'm getting the freeze 2 months in when clicking at Kunduz, a castle holding in Bactria's capital (Bactria

). Curiously, I don't get it when the game is started, just when every startup event has already happened (ie. when the first month has passed). This has happened 5 of 5 times, and the only buildings I can think of those holdings have are the cultural troop buildings and the special one for Bactria's capital (the Hetairoi)
By disabling all LI buildings, cultural troops/elite troops ones included (previously I hadn't removed them), the freezes seem to have stopped (1 year of in-game clicking holdings)... so I believe I'm on the right track when saying that our humongous number of buildings or the cultural troop buildings have something to do with the freezes.
A final note (18:20 here): Yup, it seems disabling all buildings and restoring to vanilla has stopped the freezes I was having with every holding (both Kunduz and a castle barony whose name I've forgotten at Suthseaxna) are completely gone + the obligatory year of clicking arround baronies without any freeze whatsoever... so we might have to take an extensive look at our buildings and either rework it from the ground up, saving what we can from our actual system or wait and see if RoIs patch does us any good.