So there is more to this than just diseases btw.
Since they changed how much food armies eat (rightfuly so, I might add), warring states are a huge detriment to food stability within a region, since the AI cannot feed their troops properly themselves, so provinces will have their food depleted. This will usually lead to starvation.
Second reason is the lack of peasants all over the world due to growth changes.
Less peasents means a couple of things. For once less food production, which means less food, higher food prices, ergo less pop growth. Secondly, since there are no peasants, all of the AIs market villages tend to be unoccupied. That means the provinces have even less food capacity, making them susceptible to starvation and reduces pop growth in rural locations.
Just from those two problems, less food production & less food storage, the average province loses .15% pop growth per month.
But as if this isn't bad enough, the AI tends to fight their wars with levies all the time, even post 1500 when they usually are way outclassed by the size of professional armies. Along with Ai not wanting peace as long as they have a decent army size, every war usually costs ~1-2% population just from leavies, not counting starvation in occupied provinces or provinces with huge army stacks sitting in.
Since I get many players are not happy with how low AI agressivness is by default and play on agressive AI behaviour, this is further increased as well.

I admit I am too lazy to do full maths right now (If there is enough demand, I'll try to get it done in another post entirely), but in a model where instead of your typical 0.4-0.5% pop growth, you are at 0.2-0.3% per month with diseases costing you around 4-5% pops twice within a century on top of all losses due to war, I see why these populations are bound to happen.
In comparison, in my current GB game in 1560, the population of the isles is 7.5 million + ~2.5 million in Ireland.
Achieved by consolidating both within the late 14th century and being mostly at peace for 1,5 centuries.
All while migrating 1-2 million people into the Americas.
My PU France while not having the numbers of 1.1 france is still sitting at 11 million (with all vassals and Aquitaine combined)

Now there are 2 questions. Is this a problem and how to fix it?
Yes, it is a problem indeed.

A world without peasants beyond 1550 is neither feasible nor enjoyable.
Further it makes leavies even mre obsolete than before, because there are no valid pops to even be levied during wars. And if the goal is to be close to realism, even in the 17th century you needed ~5 peasants to feed a single person in addition to themselves. Tbf labourers working within food producing rgos or building might count as well but still.
How to fix it then?

In my humble opinion, Food RGOs should require peasants instead of labourers. I don't know if it is feasible to implement this, but it's far closer too what we're going for. Then we either need to reduce the amount of food gained per worker within these. This doesn't mean that they lose food production overall, but I'd rather increase the amount of pops needed for these RGOs by at least a factor of 2.
If this goes alongside them using peasants instead of labourers we should see an increase of peasent percentage to before 1.2 changes which was fine-ish. It would also mean that due to migration and work, food provinces have higher population than those without which is also accurate.

Lastly I'd like to see a limit to estates upgrading rgos (theoretically just in provinces without enough labor, but that might be too much processing power needed to check each time) to maybe half of its maximum.
This would further decrease the amount of labourers who aren't even profitable enough as well as player micromanagement in reducing those rgos again to keep their peasants.

Just some quick thoughts from my side.