You can get the 2nd deku nut upgrade even if you have been an adult as long as you didn't get the 1st deku nut upgrade before it. But if you already got the 1st deku nut upgrade, you have to do it before you touch the Master Sword, like said before.

Actually this is one of the most annoying glitches in all the Zelda games. I forgot this one like 3 times so far and every time I forced myself to restart the gorramn game, just because I always want the 100%.