I bought Space Quest 4+5+6.All 3 games are under same box in My Account.My question is:Is there any possibility in near future to se these games in a separate boxes in My Account when bought?

I doubt it. Then gog would have to maintain three installers instead of just one.

Basically this, it's not really a big deal since the installer allows you to chose what games in the bundle you want installed anyway so say you just want to install SQ 5 then just keep the SQ5 box ticked and untick the rest and you golden.