I tried to use LockOptions with LockOptions.SKIP_LOCKED as a timeout value on MSSQL with Hibernate 4.3.11 but it seems it was ignored.

As far as I checked, it is possible to have SKIP_LOCKED semantics with MSSQL using READPAST hint (see also https://msdn.microsoft.com/en-us/library/ms187373.aspx), for example:
select top 1 * from my_table with (rowlock, updlock, readpast);
Will return a first not locked row in my_table and will lock it at the same time.