closing gui doesn't close core, if you want to end core there is a red x icon in the lower left part. think about it: you run core on the pc or n800 connected to hifi, you open gui on n900 select dir/playlist to play, and you can close remote. and later you can reopen it on another computer to change the track etc.

pause and resume should work with a single click, can you tell me more what exactly is happening? maybe it's just a bit of delay between push and reaction from core?