Is it good practice to rebuild index on FileTable? We are using Ola Hallengren scripts, both to backup our databases and for index maintenance.
We have a FileTable in our database and from time to time, REBUILDING its PK index takes close to three (3) hours, the rest of the time it is very fast.
Questions : 
is it a good practice to reindex a FileTable ?
which is abnormal, taking only a few seconds or taking a few hours ?
I have done a few searches about reindexing a filetable but have not really found anything useful.
(converting my comment to answer)

FileTable uses Filestream technology. From Paul Randal's blog - Defrag the NTFS volume if needed before setting up FILESTREAM, and periodically to maintain good scan performance. 

Instead of rebuilding, you should defrag the ntfs volume as suggested. 

Also, highly suggest to read - Best Practices on FILESTREAM implementations - by Pedro Lopes (Senior PM at Microsoft Database Systems)