Under N99panel even if a user account is empty (with minimal SSHD/SFTP flavor and disabled CronD), the latent or hidden space used by it is about 270 MB . The latent space is also used by a website/VHost, even when it is empty. It is about 540 MB
The reason for this usage of latent space is containerization, the technology that ensures isolation of user accounts and websites/VHosts with each other, thus ensuring overall security of the system as such isolation prevents spread of attacks/malware from an infected account or a website to other parts of the system, thus improving the overall security.
To reduce this latent space usage, if the server admin is the person managing all accounts, placing multiple websites/VHosts under a single user account can further reduce this usage. For e.g. if you run 5 websites under a single account, the total latent space used will be about 0.27 GB + 2.7 GB i.e. 2.97 GB . Were you to run these 5 websites under 5 different accounts, the usage in that case would be 1.35 GB + 2.7 GB i.e. about 4 GB.