Hmm. Y'know, the whole "Mathilde is basically James Bond" thing is really doing a lot to sell me on decking her out with magic items.
Bond always gets one or two sweet toys at the start of a mission that end up being vital. What I'm actually against is said items accumulating to the point of the audience/writer not being able to keep track of them anymore.
Let's see:
• The Seed is totally fine: It's a background healing item that isn't combat usable, and gives Mathilde the ability to do the insane stunts intrinsic to being Bond without dying ten different ways.
• Upgraded Armor is fine too: Bond gets improbably undamaged in fights all the time, and when was the last time he failed to stop a doom laser because he was tired?
• Branulhune can be Mathilde's equivalent to the PP9/PPK - her signature weapon, with well established bullshit potential.
I'd say that these items form the core of her "action hero package", and as such don't really count towards the "special loadout" for a mission in a narrative sense.
Bond stories usually have 3-4 gadgets total, so that's the "narrative limit" I'd recommend we stick to when it comes to Mathilde - anything beyond that will be almost impossible to work with for the author and audience.
• The Belt of the Unshackled Mountain gives her auto-retribution in both magic and melee duels, and immunity to Chaos and Fire - all of those are things I could see coming up as a Chekhov's Gun in a bond story. As such, I'd say it permanently takes up one of the "gadget" slots - luckily, since there's so many different modes that might be a game changer, it won't be getting old anytime soon.
• The Boon of Hysh item also takes up one of these slots, in my opinion - its whole purpose in the story is so that when poison comes up, Mathilde can go "luckily I had this prepared earlier!" without the audience rolling their eyes. Since it looks like we won't have to deal with Skryre or Eshin much in the future, I recommend leaving this at home to "free up" one of these slots. The in-character justification can be that now that she won't be dealing with Skryre or Eshin, Mathilde doesn't see the need to risk carrying a pretty heavy and fragile thing around all the time.
• Speed of Light and/or a huge fire nuke would absolutely fall into this category as well. It could be like that classic Bond thing where some seemingly innocuous item is actually a grenade that Bond uses to set off a chain reaction that explodes the whole enemy base.