What was the point of the Klown standing outside the convenience store and disguising himself as a moving statue, if two minutes later he's going to go into the store and start wrecking it anyway?
I'm not convinced this movie really holds up to high standards of logical analysis, it's just meant to be funny.

The dead cotton candy people have a limited shelf life, they keep the balloon people as back-up for when the cotton candy people reach their expiration date

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I'm pretty sure nothing was marketed for this movie until YEARS after.

Bunch of random marketable beep like the Xmen and Transformers. Everyone is special and you got to collect em all. Gremlins 2 did the same thing. It's just silly stuff writers in the twentieth century liked doing. Weird bunch, them monkey/future boys.

so then what was the shadow puppet thing about? it's almost like each clown had their own power set.

I've always had a love/hate 'relationship' with this movie. Yeah, it's campy but it's freaky at the same time and I NEVER understood why they didn't go around helping other people. With the whole idea,
'hey the more people we SAVE, the more people that can HELP us save more of the town!' that's wasn't tried at ALL. Especially once they realized all they had to do was hit their noses to kill them. So what if the ship was about to lift off wouldn't the best course of action would be to start saving people that seemed to still be alive, tell them how to kill a klown and keep moving?
Seriously I haven't seen this movie in a few YEARS so I don't really remember there being only girls in the balloons the next chance I have to watch it again I'll check that out! Nice detail.
3rd generation American from a long line of Gottscheers it was Drandul, dude!

Besides from the Chiodos brothers themselves I was the first to discover and find out for myself that the klowns only trap girls in giant balloons.
If you study some of the other balloons carefully enough you can tell that each one has a girl trap inside! Best ones to look at is the grey balloon during the parade where they are collecting cotton candy cocoons and giant balloons.
The other is the red balloon when Dave and mike enter into the cocoon room you can hear a girl screaming from her balloon on the right side all the way at the top!
I don't know how the klowns got her so high up there?
Some think the scream comes from the orange balloon but I'm sure it's the red one.
Also if you hunt around long enough on line like I did you will find bits of info that does confirm that they only trap girls in balloons.

I thought I remembed seeing people other than just girls in the balloons
3rd generation American from a long line of Gottscheers it was Drandul, dude!

They could also either impregnate the girls or change them into female klowns as well too! If they can survive inside their balloons long enough.

More diabolical plans for later eating on their home planet for more klowns to chow down on.
3rd generation American from a long line of Gottscheers it was Drandul, dude!

The could not really wrap the leading lady up in candy floss, could they? That would have killed her.