The answer to that varies by unit.
Nebula and its Spicula drone appear in the campaign and a (possibly no longer functional) standalone mission. A shielded air unit poses some balance and design issues so it's unlikely to make it into the core game in its current state, but it is functional as a unit.
The Sunlance turret (an unused building) also appears in the campaign. Sunlance acts a lot like a stronger, more expensive Stinger, so those two turrets would step on each others' toes if they coexisted in the core game.
Sonar Station (the other unused building) used to be in the game, but when sea mechanics were reworked it was no longer needed. Similar applies to Surfboard, a sea transport which was very rarely used and required a disproportionate amount of dev work to keep bug-free.
Most of the others are models in search of a purpose. Every so often there is talk about putting a Kestrel-like unit in the game; it may happen someday. Lancelet was considered for addition in the ship factory rework some years back, and if a second primarily-water factory is added someday it may find a place there. Eclipse is an interesting visual design but as a unit design hews a bit close to Likho. Vanquisher's model is basically two Corsairs smooshed together, so it's unlikely to make it into the game.
Trisula, Morningstar and Daimyo actually are used in the game, sort of; Bolas is much like Trisula but with a different weapon, and Siren combines the model and secondary weapon of Daimyo with the primary weapon of Morningstar.
The unused chicken units are probably leftovers from a chickens redesign.
