if this is allowed by FIDE rules to have games played without clocks for FIDE rated events
The answer is that, yes, this is allowed. FIDE used to rate tournaments not games but for many years now that has been reversed and FIDE rates games not tournaments. So, individual games that are played by FIDE registered players using clocks in an event which has been registered for FIDE rating will be rated by FIDE and games that do not satisfy all the necessary criteria will not be rated.
Normally it is the responsibility of the chief arbiter and the federation responsible to only supply valid data to FIDE. That is, the games which don't qualify for FIDE rating should not be reported in the TRF16.
The part of FIDE which is responsible for ratings is the Qualification Commission and as you can see from the link the current chairmen is Bermudan Nick Faulks.
Here is Nick commenting on another matter (what happens when the arbiter repairs two players whose opponents didn't turn up but gives them less time than for the competition as a whole) in the English Chess Forum in 2013 making the point that FIDE rates games individually.
At first I was puzzled by this discussion. FIDE rates games individually, so a game is a game. But how do you report it? In a given round, AvB is 1-0 def, CvD is 1-0 def, but then the game AvC takes place. What has happened? If that game, because it starts late, is played under a faster time control, that may also be a problem. I don't know the answers.