This is generally intended; all Niagara Systems require an Effect Type to be applied in UEFN to pass validation. In previous releases, there was an issue with the validation system that allowed Niagara Systems to be uploaded without an Effect Type in place, which could lead to content that will now throw errors.
A question remains whether in some cases the Effect Type was set, but then got automatically cleared somehow. If it got cleared by mistake, this is indicative of a bug that we need to address, but we don’t have any indication of that so far.