There is only a glitch for the Deku Nut upgrade at the Forest Stage. The Deku Stick upgrade can be obtained from the Forest Stage at ANY time in the game. I've just played this part in OOT on Wii Virtual Console (& this was actually the first time I heard of this glitch - after playing OOT for 10 years! I guess there's always something to be learned from that game!)

As for the Ice Arrows, you CAN get them, even if you unlock different doors in Gerudo's Training Ground. There are enough keys in within it to unlock all the doors. I just did this in my file on VC, because after playing OOT so many times, I thought it would be fun to try out the different doors, but little did I know that only 1 path leads to the Ice Arrows, so that forced me to hunt down ALL the keys. You can get the Ice Arrows without getting all the keys, but there are still enough keys to get them all.