I don't know too much about the traditional way to keep weapons, but I use the useful way to keep them from breaking, cracking or tearing holes in my weapons bag.
That is especially for the bokken and tanto since the jo has the same ending on both sides.
If I take them out of the bag, I keep the "bladed" weapons with the tip pointing up. Two reasons- 1. keeping the tip down wears it and it starts to chip. 2. with the tip down, the weapon is less stable and has a greater chance of falling and by that getting unwanted hits...
As for the bag, when I started weapons practise I made a special bag for my weapons, with two layers, cross- stitch work, a small compartment for the tanto etc. A friend from the dojo who saw it told me- if you want that bag to last longer, keep the balded weapons pointing up, or they will start to tear the bottom of the bag. It's still holding!