In the vein of the R&D materials tab - one dedicated exclusively to non-combat pets (deployment limits still apply). This should be simplicity itself to implement.
And to help populate that tab, might I suggest a set of pet packs associated with the various 'headhunter' accolades? For instance, destroying all the named Tarantulas (spread across Vault: Ensnared, Fed. Fleet Alert, and Tholian Red Alert) would give you a pack containing a pair of miniature Tarantula pets (one space, one ground).
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STO Resources: <Ship Comparison - All Tiers + Small Craft + Hangar Pets> <Damage Resistance>
<R&D + Upgrade Costs> <Duty Officer Finder> <Suliban Doff Reqs> <Fleet Costs> <Rep Costs>
<Keybind Tour the Galaxy> <Fleet / Armada Management> <Currency Exchange> <Other STO Links>