E1A officially still exists as the easternmost gate in Terminal E, in the area of the C-E connector amid what used to be the domestic E gates in the former Terminal D area (most of which are now in Terminal C). It doesn't appear to be a fully-functional gate on Google satellite views, and given that I know Cape Air has used it at times in the past, it might be a non-jetbridge gate and/or used for bussing to stands.
E8A, unlike E1A, doesn't appear on the Massport terminal map. I know there used to be an E8A gate designated (in the vicinity of what's now the A380 gates) back before the gates were renumbered during one of the renovations, so either there's still an unmarked E8A somewhere or its a FlightAware glitch.
NC3 (or, well, anything NC) isn't a gate as such, it's a hard stand in the North Cargo area near the general aviation ramp on the other side of the taxiway northwest of Terminal E. Some of the international heavies do wind up out there. I believe in such cases the passengers are bussed to the terminal, though I couldn't say if those operations are a capacity thing, a cost thing, or both.