Right after they trapped Debbie in the balloon, why were the Klowns so quick to flee the moment Mike and the Terenzi brothers arrived at Debbie's house? Considering their almost Nigh-Invulnerability, what could be so threatening about Mike and his buddies? Well, if you pay attention, the moment Slim sees the ice-cream truck he goes "uh-oh", rapidly blinking as in disbelief, then quickly getting into the Klown car to escape; it's not Mike and the Terenzi brothers they're afraid of, it's the ice-cream truck. Probably thinking a rival to Jojo the Klownzilla has come, this serves as a subtle foreshadowing for when the truck is used to stall the Klowns just before Jojo's arrival.
Crescent Cove features carnival fairgrounds, which is why the local burger joint and ice cream truck are carnival and clown themed. It would also explain why the locals aren't very surprised to see clowns walking around.
The Killer Klowns land in the town of Crescent Cove because it has carnival fairgrounds, where they can hide their mothership. However, they first land at the local make-out point. When they venture out into town, it's apparently still pretty early in the evening, given that the burger joint is crowded. The Klowns relocate to the carnival later on, when the carnival is closed. They were presumably waiting for the carnival to be deserted before arriving to maintain their cover.
"Why clowns?" Well, given the Klown's aggressive and sadistic behavior, their bright, clown-like appearance may be an example of aposmatism, or warning coloration.
It's implied the Klowns were the inspiration for circuses, human clowns, and coulrophobia. At circuses, people usually watch clowns act like buffoons and eat popcorn, an effigy of the Klowns young/eggs. It's quite possible circuses started as a Wartime Cartoon-esque Take That! to the Klowns.
Fridge Horror
Since Mike suggests that the Klowns may have inspired humanity to create the clown figure by visiting the Earth in ancient times, it's easy to imagine that perhaps at some point in prehistory the Klowns may have hunted down our ancestors, explaining why many people fear clowns today: it's not an irrational phobia, it's a repressed survival instinct.
To add to that idea, perhaps Egyptians made mummies, a form of burial involves wrapping up the dead, to mimic the way the Klowns capture and kill humans with the cotton candy guns as an attempt at negotiating with them for survival and worship. In fact, many believe the prototype of clowns came from entertainers of Ancient Egypt, usually Pygmies and other individuals of short stature who were seen as people with celestial gifts; even respected priests also partook in being jesters to serve a socio-religious and psychological role.
On the other side there's Loki, a god of mischief whose biggest note of interest is being a troublemaker who brought on Ragnarok. He is what the Klowns are described as through generations of word of mouth and mistranslations.
While the popcorn Klown-snake spawn at Debbie's house would probably get exterminated by the police or the military, they'll hardly catch those that Jumbo sprinkled in the fast food's dumpster. Furthermore, if Jumbo randomly decided to sprinkle the popcorn in the dumpster, there's a high chance that he may have seeded more of those little bastards in other random places around the town.
With Word of God teasing that several Klowns survived (by presumably abandoning the ship before it tried to take off and exploded with Klownzilla's defeat) this could mean that said Earth-bound Klowns are still out there hiding, and possibly raising the popcorn Klown spawn into new recruits for the day they decide to strike again...
Klownzilla is seen to be controlled by strings. This implies he's a puppet. Which implies the existence of unseen manipulators so gigantic or powerful an 18 foot tall Klown is a toy to them. Think about that.
Perhaps that threw the acidic pies at the protagonists in the ending.
