Low% means finishing the game with as few items as possible. Or, in other words, skipping as many items as you can. This means that you sometimes have to go out of your way in order to skip one item. Naturally, that is slower and thus, low% takes longer than any% (which means beat the game as fast as possible, no restrictions). Compared to optimal any% with sail and quiver/light arrow skip, this route also skips obtaining the hero's sword.
This is specifically a 9 item route, and currently the game has been beaten with 7 items: Wind Waker, Bombs, Bomb Bag (30), Deku Leaf, Single Magic, Hero's Shield, Uncharged Master Sword. The big development was skipping the Mirror Shield and Fully Charged Master Sword (by unloading the Ganondorf Cutscene after setting up Actor Unloading with PROC_ROOM_SCENE corruption). In theory a lower item count than 7 could be achieved through the use of Hyxost Bombs but this is currently the RTA limit.