What determines the differences between a bag of holding and a scroll case?
What prevents a sword from being placed in a scroll case and what determines how much that item can hold?

I checked DLTCEP and NI but I can't seem to see any real differences besides some texts and bams.

EDIT: I guess I really do not care if a scroll case will hold a sword or not my main concern is the amount of holding. I baseicaly want it to hold only 20 items. so if someone could point me in that direction

The corresponding .STO (store) file. They always have the same name: item and store.

For example:

Bag02J.ITM (of the Categories - Containers *36*, offset 0x1c)
Bag02J.STO (of the Categories - Container *5*, offset 0x8)

In this STO file you can check what you wish:

1. Store purchases (0x9c --) - here go your restrictions for the items (weapons, scrolls, whatever)
2. Storgage capacity (0x22) - max number of items (put 20 if you wish).

I'm sure dltcep supports store capacity

oh heh thanks I did not even think to look in the store files. thanks.