The SNES version had a very clear weapon progression. One of the changes with SR:R is that you are now free to use whatever weapons you want. Merchants will be adjusted accordingly. The only weapons which will remain the same are those received through plot means.
The dead body of Decker has the Beretta. This will be replaced with an appropriate Light Pistol (or equivalent).
If you “forget” or “misplace” the Beretta Glutman will give you the Zip Gun. This will be replaced with an appropriate Hold Out Pistol (or equivalent).
That being said, we will use out of the box weapons (unless plot dictates otherwise). The relevant merchant will have an expanded inventory list on their own wiki page and this page will not be updated.