Most likely because the simulator isn't multi-threaded, the most effective course of action would be to use Task 7 to check for pending characters on a 68K side loop, and implement your own numeric input routines using Task 5.
You could of course also look at the source, and pump the simulation instead of blocking on OS calls.
The problem with not servicing interrupts probably effects any OS task that might block, for instance writing data to a file, or displaying a file dialog.
DC.L INTA ; IRQ1
START: ; first instruction of program
MOVEQ #7,D0 ; Check Character Pending
MOVEQ #5,D0 ; Get Character
TRAP #15 ; halt simulator
INTA EORI.B #%01010101,$E00010
END START ; last line of source