Road numbers very rarely reflect a road's place in the highway network of the US. In the age of digital maps and GPS, road numbers on minor collector roads like these are a relic and mostly reflect how a road is maintained (in this case, by the state) rather than how important it is. Route 96 only links to some small rural neighborhoods around East Boothbay, without any connection to other secondary or tertiary roads. Ignoring the designation, that is enough to conclude that secondary is overkill for a no-outlet rural highway, and small-scale edits like these don't necessarily need to be discussed.