1) mdbx is really fast. Like, really fast. Even amongst general memory mapped databases, it is very fast. SQLite is anything but - it is not even really meant to be used this way.
The problem with MDBX however is that it's still being actively developed and that it is prone to randomly losing your data. Maybe not anymore, but especially the beginnings were very painful. What's "worse", in case you do lose your data somehow, you have to rely on MDBX's own data recovery, which may but also may not work. It is also not really possible to see the content of the database unless you reimplement the way Miranda accesses it.
With SQLite, there are billions of such tools for recovery, moreover the format is a lot more "stable" so to speak; and to top it off, you can take a look at the db contents anytime you want because it's just standard SQLite database.
As most people prefer data integrity over "speed", and after the many pains of MDBX, it was decided that SQLite is the way forward.
I'm sure there could be some improvements to startup times though (where a lot of random access to the "rather large" miranda database happens. I suppose this is a topic for discussion. Maybe MIranda could implement some kind of startup cache DB?
A smaller profile with only the data Miranda needs at start? Who knows what the future will bring.
2) yes, SQLite db will on average be about as much bigger as you have seen. My profile was around 530MB and now it's 675MB.
3) Compacting works for me. Might be worth trying to reimport your profile (after making a backup).