When they were first introduced, the initial purpose of the "Mist Well" furniture items for guild halls was to enable their members to refill their Mist Energy tanks, due to any member (or multiple members) of a guild "donating" enough Crystal Energy to help keep the well active. With Mist Energy no longer a part of Spiral Knights, the requirement of a user having to deposit a minimum of 500 Crystal Energy is as functionally redundant as the "minimum withdrawal limit" of 100 Crystal Energy.
My suggestion is that these "mandatory limits" be permanently removed from this item, so that guild members can deposit whatever amount(s) they choose, as well as enabling them to withdraw only what they need. There is no longer any reasonable purpose for "Energy Wells" to have these unnecessary "limitations", so it only makes sense to get rid of them.
I don't think the energy wells make that big of a difference or any difference, but I mean why not have them be a bit of a useful feature. I also think it would be nice if they were made to work like they were originally intended to a bit- you put in a large sum of energy, and you get more back out slowly. Of course with just one type of energy, feedback loops and energy farms would need to be prevented, possibly by making some kind of energy coupon that took 100 CE off of a purchase.
But as of now sure, this would be fine and good, and you're right.