On the Boeing 737 NG:

ALT ACQ is always armed when flight directors and/or autopilot is engaged in a climb/descent mode (V/S, VNAV, LVL CHG, TO/GA, CWS P), it is however, as you suggest, inhibited in G/S and G/P (glide slope, glide path) modes.

On a typical ILS, I would typically set the missed approach altitude (which would be captured during missed approach in TO/GA mode) on glide slope capture. You could also set the missed approach altitude when ALT HLD is engaged, and you know that you will not need to change altitude again until when intercepting the glide slope. (When changing the selected altitude with ALT HLD engaged, the "held" altitude is maintained, until a new vertical mode is engaged, regardless of selected altitude).

HOWEVER, performing a Non-ILS approach in V/S or VNAV, the set altitude WOULD be captured on descent. To avoid this, the approach MDA is usually set on the altitude selector, and kept there until sufficiently (typically 300 ft) below the missed approach altitude. When passing through this altitude, the missed approach altitude would be set (logic is implemented to make sure the altitude is not captured during the "winding up" of the selected altitude).

Lastly, performing a Non-ILS using IAN (Basically Boeing's solution for performing Non-ILS with ILS display and control laws, using FMC data), the final descent would be performed in G/P mode, which behaves roughly like G/S mode, eliminating the use for initially selecting the MDA.