Fresh install to OMV7 (from OMV4) - What about my Data-Drives?

Quote from lev

Can I also format the current system SSD first during the installation so that it is completely empty?

Yes. However it might be helpful to have a backup of the drive. Just in case something unexpected happens and you would like to go back.

Quote from lev

What do I do with my mounted HDDs (48 TB of data)? Should I disconnect them from the SATA controller beforehand and plug them back in after the installation is complete?

Yes

Quote from lev

Doesn't OMV want to format them first?

No. After the fresh installation you can mount them.

If you use RAID you have to install the openmediavault-md plugin first.

You will have to do the complete configuration from scratch. For that it might be helpful to have screenshots of your configuration and a copy of config.xml for reference.

In any case you should have backup. Always.