The way Spotlight works on a Mac server is that -
- There is a special server process running to do the indexing automatically - normally by monitoring file system changes i.e. modifying a file or creating/deleting files
- The use of a special Spotlight system account and the automatic addition via ACL records to allow this system account to have access to every file and folder
With a server obviously the usual situation is that there are multiple different users and each user normally has different access permissions such that userA may not be able to access files owned by userB. Therefore userA is not going to be able to access and index files restricted to userB, hence as described above the special Spotlight system account on a Mac server.
Spotlight on a Mac server is also clever enough to not only be able to index files owned by everyone, but to also only return the search results that user is allowed to access, therefore you will not see in the list of results files private to other users.
Realistically this sort of system has to be done on the server itself, therefore it is the server supplier who has to provide this capability. So in your case QNAP.
Unfortunately Spotlight is proprietary to Apple so no-one else can add it to their product. You would still be able to do a basic filename search but not a file content search. There are some third-party products you can buy which can do their own file content indexing and these provide their own search clients. I used to work for a company and run the IT for them and we used a tool called 'Sonar' which did this. See http://www.virginiasystems.com/products_s.html (I would not advise buying this particular solution now - it is possitively ancient and Spotlight would be the better choice.)
A possible option would be to have a Mac server and have the Mac server mount the QNAP as a drive, and then have the Mac server re-share the QNAP. Mac clients would then access it via the Mac server. The Mac server would then handle all the user-authentication i.e. logins, and would also do the Spotlight indexing. This would add a network traffic overhead and this could be reduced by having two network connections on the Mac server, one to the LAN with the Mac clients, and a second dedicated on just to the QNAP.
Some people use iSCSI or NFS to connect to the QNAP (or similar NAS system), while the Mac clients would use AFP or SMB to connect to the Mac server as normal.