There are a couple of different ways this logic can be implemented in Simulink :
1. One can implement a counter logic which increments its value every simulation step ( so every 2 seconds if say your Simulation Step size is 2 seconds) and write the value to a data store. The motor controller can read from this memory location every time and figure out the time since the last time the motor was turned on (or some such equivalent value). Of course you would reset this memory value according to your needs (e.g maybe every one hour). Now as far as this working on a real-time system, as with any generated code from a model you need a scheduler that calls the simulation every fixed-step size seconds. So hook the generated code to up to a scheduler that calls it every 2 seconds and you are all set.
Note: This will implement the logic you desired, but one situation to consider might be the following:
If your motor has been idle for 58 mins and then turns on (and off) 6 times in 1 min (chattering), the above logic alone will not help in preventing this. Additional logic might need to put in to safeguard against this situation.
2. Another idea that can be considered is that you can have first order dynamic system that basically ramps up as time goes along (according to its time constant) and gets reset every one hour (say). You could use the output of this first order system to make your ON/OFF decision for your motor in a sort of similar way as above.
