I have just purchased the final weapon from Ms Zirkon and I did not get the trophy for unlocking all of the weapons in Rift Apart. I have completed the story and I am just finishing up some final side quests now. Has this trophy glitched out on me or something?
There will be a special weapon unlocked once you collect all of the hidden spybots. You need to return to Ms Zirkon when you collect the final one and she will build a weapon that you can purchase from her. I got the trophy when I bought this weapon.
I also found two new weapons when I started the game again in challenge mode so you may need to do this to get the pixilizer and the pirate cannon weapon. Check out this weapon guide for Rift Apart and it will cover the list of all weapons that you need to own to get the trophy.