That's the one drawback to Liana's Toolbag, it hindered the usefulness of pets like Cats' resource ping.  It would only ping resources for the current tool you had equipped, but the bag equips every tool.  So even if you are just looking for Wild Herbs and the like to gather, you'll still be pinging every unwanted rock and tree in the area.

Take the tool you want to use out of Liana's Bag.  Equip only that tool, your pet works again.  

Unfortunately that still doesn't solve the issue of targeting. If I only want coral reef and giant claims, the pet will still highlight every starfish, algae, and turban shell in the sea. Same thing goes for targeting a specific kind of tree for sapping.