Does seismic charge detonate when you drop it on a ship or a ship flies through it? Like, for instance, proximity mine.

From the Seismic Charges upgrade card:

When you reveal your maneuver dial, you may discard this card to drop 1 seismic charge token.

This token detonates at the end of the Activation phase.

When this bomb token detonates, each ship at Range 1 of the token suffers 1 damage. Then discard this token.

It doesn't care if it hits a ship on its way out of the bomb chute, and it doesn't care if a ship overlaps it during the activation phase. It only cares who's close to it at the end of the activation phase, when it detonates.