The real question is can Windows defender scan these drives?

I don't know what it scans by default, but it can custom scan mounted volumes with no visible mount points assigned at all, e.g., my EFI partition:

  PS C:\Users\jtm> & 'C:\Program Files\Windows Defender\MpCmdRun.exe' -Scan -ScanType 3 -File '\\?\Volume{91ada2dc-bb55-4d7d-aee5-df40f3cfa155}\'
  Scan starting...
  Scan finished.
  Scanning \\?\Volume{91ada2dc-bb55-4d7d-aee5-df40f3cfa155}\ found 1 threats.
  Cleaning started...
  Cleaning finished.