In March, Zayn quit 1D after five years, explaining in a statement that he wanted to "be a normal 22-year-old".
The band – Harry Styles, Liam Payne, Naill Horan and Louis Tomlinson - said they respected his decision to leave but would continue as a four-piece.
Speaking on US show Extra, Simon said: "Well, I don't think they'll ever be over it completely because they started off as a five piece, so they're always going to miss him... But it happens."
Despite 1D now continuing as a four-piece, Simon said they are now much stronger.
"You've got to dig deep and you rely on each other," he added. "In a weird way they kind of got stronger through it."
In an interview in May on The Late Late Show with James Corden, 1D said they were initially "angry" with Zayn for deciding to leave.
Liam said: "Like I say, we were angry at first, but then it was just a bit more disappointed, but we wish him the best of luck with whatever he gets up to and there's no hard feelings. We're just going to carry on as usual."
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