You will likely have issues if you ever try to sell property with an unpermitted well. FHA loans have restrictions on the well as do many local jurisdictions that may refuse to convey the property if the well isn’t up to code. My local jurisdiction won’t block the sale but will write an alarming letter to the seller. In the case of a new build or major remodel, you will not be able to get a certificate of occupancy without a state and county verified well here.

> Hell most of the licensed contractors I hire (electric, plumbing, etc) don’t bother to pull permits, even for new work.

Yeah, it’s your responsibility as a homeowner to get the permit (either get it yourself or see that the contractor does). Even if you don’t think the permit inspectors are doing anything in terms of quality control, the permit helps you to pass inspections as part of the sale process and will limit your insurance exposure if there’s ever an issue. There’s probably fine print in your insurance contract saying that all work shall be permitted as required.