On every file change ST status bar says - indexing files. And it takes > 10s (I have a lot of files). When it does that - 2 CPU cores are loaded at 99%.
Opened the console (@jskinner suggested to enter sublime.log_indexing(True)) and there was a message that index is corrupted and I have to remove it. Index is located in:
/Users/bumbu/Library/Application Support/Sublime Text 3/Index
Removing all the files from that folder did the trick.