If I have a magic secateurs in my inventory, and a regular secateurs in my toolbelt, do my magic secateurs get priority? It's hard to tell now that they've changed the animation. Also does this go for all other related tools? Or do you have to be wielding the item in order for it to take priority?

I'm fairly certain magic secateurs effect only works when wielded and always has been that way even prior to toolbelt hence farmers wearing them or equipping them when arriving at a plot despite use mud staff or w/e for teleports/compost etc.

 

As for tools that do not require being wielded it's same rules as always: the best item takes priority.

If you wield mith hatchet, have a d hatchet and got bronze on your belt you will use d hatchet.

You can't use regular secateurs to pick herbs or allotments or hops. They're only used for pruning tree branches, and magic secateurs are identical to regular secateurs for pruning tree branches. The magic secateurs will take priority for that, but it won't matter because they're the same. And for anything else, there's no priority to take because regular secateurs can't be used at all.