Rewire Harddisks: Is my assumption correct that Linux does not care where the disks are connected?

You are correct. Linux does not really care where drives are connected, and you do have to make sure the drive with the OS on it is in the boot order set in the bios.

There are a couple of things to consider though regarding hardware and where drives are connected. (this is for you and for anyone else that reads this).

Some motherboards (particularly older ones that may be re-purposed as a NAS now) may have different speed sata ports. There might be a couple of SATAIII and a bunch of SATAII for example. Try not to mix the ports on a RAID if you can avoid it. This is simply to optimize performance. A RAID will only operate at the speed of the slowest drive, so one of the faster ports may be better used on the system drive or another stand alone drive.

If your board is using an nvme drive, on many boards these often disable several onboard sata ports to use the controller for the nvme, so in this case it would matter where drives are connected, since using ports the nvme disables is not possible.