Actually, I found them more useless in MM than I did OoT. I relied heavily on bubbles and rarely used the nuts.
And they are quicker than the hookshot, because there's no penalty of having your hook go too far.
I think the only times I've ever used the Deku Nuts was by mistake. I have never really felt the need to use them, and mostly when I go to the Inventory Screen, I just skip over them, like they aren't even there. Barely ever think about them throughout the entire game.
I only ever used them on Gohma the first few times I played the game, then I realized how much easier the slingshot was (first zelda game I played - and I didn't realize most bosses in zelda games are vulnerable to that dungeons treasure)
Well some enemies would run around in circles making it harder to attack them without them dodging or you just got tired of chasing them. The deku nuts came in handy when you just wanted to get the kills over with faster.
Well honestly, I have never used the Deku Nuts. They seem to be the second most useless item. All they do is stun, and then when you hit the enemy, they unfreeze. I will never get why they included the Deku nut as an item.
I don't generally use them much, but in my recent playthrough, I've been making an effort to use them (and some other items) more. I liked using them to stun Skulltulas for a while, before I got the bow and could just take them out in one hit.