The shelter was supposed to be like a bomb shelter right?
The name is important, because no one in the game calls it a "bunker" , which are more elaborate, larger and expensive, usually privately owned.
A "shelter" implies it's supposed to be something smaller, short-term and meant for the public. Usually, it's ok for people to just go into a shelter anytime and just fuck around as long as it's not during a disaster.
I'm thinking before a Dark Fountain was opened in the shelter, it was originally a small space that the kids used as a hideout. Kris, Dess, Noelle and Asriel played pretended that the shelter was way bigger than it actually was, because everything is just bigger when you're a small child. They would roleplay the shelter being a secret underground hideout, or a massively sprawling dungeon.
In reality it was one room, but kids have vibrant imaginations.
At some point, Gastery-shenanigans happened and the kids' imaginations became reality via the creation of the first Dark Fountain. Dess disappearance happened and this was how the shelter became a dangerous thing that needed to be locked up.