An evil doer has created an app to detect superheroes and clay puppets just happen to be his choice of minion.

Of course clay puppets are his choice minion.

Are these bi-sexual secret super-heroine strippers?

She dated the evil doer in college. She used to make fun of his clay making.

Now that he has discovered the secret of bringing clay to life, then killing it, then making it resurrect into an undead form, he plans to kidnap her for torture and stuff and to gloat. Unbeknownst to him, she has gained super powers.

It is just a coincidence.
The clay puppets simply do not approve of strip clubs because they perpetuate undesirable sexual stereotypes. They intend to destroy the place.
Interestingly, they have gone rogue and are free lancing.
Their evil master loves strip clubs and visits such places regularly.

They are tired of being discriminated against by society and decided disregard the porter and just walk in to enjoy the sight of half naked women.

Kinda sounds like something outta Silent Hill…the puppets are a physical manifestation of the locked secrets, dancing like mad to be released, but are enclosed in a vile prison of complete debauchery.
You must realize your demons, and then conquer them. That’s why they’re here. That’s what they’re supposed to mean. But a realization will only be made by the women through a rough ordeal, wrought with dark revelations, and things best left in the dark.
To learn of the language of the puppet and free your soul, you must dance with them. Explore your creepy past, why do the women hide their very essences behind superhero identities and sex?
What lies beyond social structured facades that is so important to discover that dancing puppets would appear? And why those chicks? Isn’t everyone fucked up in some way or another? The puppets were sent by a messed up abandoned town, which is actually the Bermuda Triangle. No one knows if it selects specific people or does it randomly. Some people can find it, others not.

Look closely by your bed or in the kitchen when dusk covers all with darkness…maybe there’s a puppet, or some fat guy throwing up in your toilet.

When you have two protagonists sharing a secret that neither knows about the other then you need the clay puppets to break in to strip club and stir up shit. How else do you get your co-heroines to share a meaningful, “we need to talk about this later” look right before they kick some Howdy Deady ass?