Would it make sense to still allow the bonuses of Thieves' tools when trying to disarm it or is there some other item or skill (such as Arcana) that would apply?
Those two cases are not mutually exclusive.
Let's address the skill first, because that's an easy one.
Any character can attempt an Intelligence (Arcana) check to detect or disarm a magic trap, in addition to any other checks noted in the trap's description.
— DMG P 121
So, yes, they can use a different skill.
Would it make sense to still allow the bonuses of Thieves' tools when trying to disarm it
I'm going to address this from two different angles. First as a game rule (i.e. what do the rules, as written, say):
Proficiency with these tools lets you add your proficiency bonus to any ability checks you make to disarm traps or open locks.
— PHB p154
So RAW says "yes".
… but a player who trying to claim a bonus for simply having them would have be calling shenanigans. It doesn't make much obvious sense from a fiction first perspective.
I'd ask the player to describe how they were using the tools to help them before allowing the bonus. They'd be welcome to invent whatever details they liked, just so long as they justified it.
OK, so, I take a deep breath and spend a moment steadying my nerves. I don't want to have wavering hands for this. I take the copper wire in my pliers and carefully touch one end to the axial manna node and the other to the detection symbol — making sure not to put my hands over the glyph — that should short out the arcana potential and dispel it.
Of course, if they came up with a sufficiently good explanation, I might go past giving them proficiency and skip the die roll entirely:
In most cases, a trap's description is clear enough that you can adjudicate whether a character's actions locate or goil the trap. As with many situations, you shouldn't allow die rolling to override clever play and good planning.
— DMG p121