I am considering to watch The Zeta Project from the DCAU but I don't know much about it and I didn't watch many episodes from Batman Beyond (including Zeta ones). So can I enjoy it individually or should I look back to some other DCAU stuff before it for better understanding?
As cde puts it, you can watch The Zeta Project without having watched all the Batman Beyond episodes. It's mainly because it is a spin-off series based on the character Zeta from the Batman Beyond episode named ZETA season 2, ep 20.
Thus, to answer your question, you should start watching it as it's remarkably interesting (in my opinion). But, there are a few cross-over episodes like Shadows which might have Batman Beyond as its pre-requisites:
Batman (Terry) and Bruce view security footage of a mall's destruction and based on the incomplete footage, they believe Zeta to be responsible.