Hi Tobias,
As far as I can see, the drop-down box is filled with all FTO for which the user has "Display" access for Authorisation Object GTS_CD_FTO. So you should be able to control the visibility by restricting that access.
Restricting in that way would affect the Export, Transit and Periodic Declaration tabs. If you need to control those tabs separately, then you'd need to create a Code Enhancement in Form FTORG_LISTBOX_FILL (program /SAPSLL/LCORE_LEGAL_MENUEF02) to delete selected entries according to some logic, when IV_ID has the value /SAPSLL/MENUE_CUS_0711_S-LIST_FTORG_CREATE.
Hope that helps.
Regards,
Dave