Assume you are playing Standard American (a natural system with 15-17 1NT openings and 5-card majors), IMPS, and nobody is vulnerable.
Some background. There are some situations where your partner has suggested playing in notrump. You have the values for game and you're pretty sure there is no major suit fit so you figure you might as well bid 3NT. The opponents attack your weakest suit, and although your partner has the suit stopped, the stopper is knocked out immediately and your partner cannot take nine tricks without losing the lead, You are set, and the result was almost predictable. This is IMPs and there is no shame in playing 5C or 5D if 3NT looks dangerous and 5 of a minor has play. However, if your partner is well fortified in your short suit, 3NT is a fine contract where partner's wasted values in your short suit make 5 of a minor a poor contract.
When you've bid two or three suits, and the weakness is in one of the unbid suits, it is very likely that the opponents are going to lead your weak suit. It is optimistic to just bid 3NT and hope that by not giving the opponents information, they will lead your longer and stronger unbid suit.
You have a maximum 2D bid (you expect your diamond suit to provide several tricks) and want to accept game. However, it is not your best choice to say "I'm bidding 3NT - the club stopper is my partner's problem."
A better call is to bid 3H, which is clearly forcing. You are accepting the game, but you are telling your partner that clubs could be an issue. If your partner has ♣Qxx, or if he has ♣Axx and doesn't think you have nine running tricks, he probably doesn't want to play notrump.
Your doubt about notrump will pay off if these are the hands:
In 3NT, the opponents will lead clubs and will take four club tricks upon winning the ♦A. 5D is cold.
However, your partner might have clubs well stopped in which case 3NT is indicated.
Here 3NT is a great contract while 5D loses three aces off the top. You stated that your fear was clubs, and partner has them well under control and bids 3NT with confidence.
By the way, in the above auction, a 3D rebid (1D-1S-2D-2NT-3D) wouldn't have shown doubt about the unbid suits; it would have shown doubt about making a game. South would be declining the game invitation and choosing to play in 3D rather than 2NT. On the other hand, a 3C rebid (1D-1S-2D-2NT-3C) is more valuable as a forcing bid pinpointing a fear of hearts in notrump than it is a suggestion to play 3C.
3S = forcing; doubt about where the hand should be played