Ya, the numbers thing seemed pretty clear, no secrets, nothing hidden...
The Great Deku Three was one of my favorite dungeons in the game. I especially remember it when I first got the game. After a few hours of wandering around the Kokiri Forest getting used to the controls and figuring out what to do, I ended up in the Great Deku Three. The thing that I enjoyed most about it was that the puzzles were so primitve, but because it was the first 3d Zelda title, they were all fresh. Even simple things like just shooting the 'eye' above the door with the slingshot... or shooting the ladder down with the slingshot... or jumping across shallow water to light spider webs, etc... So many of those little puzzles that have been used in 2d games, and/or have gone on to become stables of the Zelda series. All started in the Great Deku Tree. Good Stuff.
The number thing was pretty obvious, I think they just wanted it to sound riddle-like.
I really liked the Deku Tree too, it was an awesome first dungeon. Even though it was a bit easy. Although I do remember getting stuck on two different puzzles: the one where you need to light a torch by catching aDeku stick on fire, and the one where you needed to dive down underwater and hit a switch, so you could get past the rotating spike thing.
It really is nothing, don't think it means anything.
I have seen stuff like this before in the past Loz games, it is really common. I can't quite remember, but I think Kaepora Gaebora spoke kinda like that, he was a very wise owl. Usually, wise people talk like this.
In this case, the Deku Scrub was obviously not wise, but there is a possibility that he could be talking to you like that so you can remeber, but I doubt that.