Which is better APFS or APFS Encrypted?

This really depends on what level of security you want and makes you comfortable. Doing any sort of encryption or FileVault setup do have some side affects like near impossible data recover (if there was a hardware issue) and if passwords are forgotten you'll most likely have to erase the drive to proceed (so data loss again). As it is meant to protect the data.

mind you encryption only help if somebody get physically hold of your computer,

if somebody trick you into executing code on your computer encryption will not have any effect

Encrypted. Depending on what level of security you want. What level of data protection.

Encryption offers a higher level of security. Personally I never encrypt my drives because no one other than myself has access to them. If that were not the case, I would enable FileVault.

If you consider the information on your Mac private and you want to ensure its security, then use encryption. If you don't care, then it doesn't matter.

simone.crete wrote:

What are the issues with APFS encrypted?

I wouldn't know. I've barely used APFS much less APFS encrypted.