Should bestiary include inhabitants of the settlements or it should not? And if should, is it possible to slightly bend the rules and increase number of monsters? About encounter tables- can I make multiple tables each for section of the map and dungeon, if I can, does it mean for each section or dungeon i must make table with at least 1d20 encounters? Should I even use 1d20 tables? Or can I use 3d6 or any other system of determining encounter?
The bestiary is for monsters. (Specifically original monsters that you wrote, not existing things like skeletons/ghosts/wolves/etc. Those you can just say "stats as [monster name]" for in the room or hex key.) The folks living in the towns are npcs, so put the details for them with the town.
The idea with the encounters list was to have at least 20 different things you can run into across the whole hexmap while you're doing overland travel. If you want to write more than that, go ahead. Dungeons should have their own lists of things in them that you make when you write them and the list size for those can be whatever you decide.
You don't need to mention stats or precise mechanics. "Stats as [monster name]" means you literally write just "stats as" plus the name of the monster. The folks reading it will pull the actual stats for that critter from the system of their choice when they run the hexcrawl. So if I wanted an encounter to be monster dogs, the list entry would read "pack of 1d10+10 Mutated Hounds (stats as Wolf)".
