TL;DR
Warn the player when a crafting entity's quality bonus is being reduced by speed modules/beacons.What?
When placing a quality or speed module in a way that the quality bonus is reduced, show a warning (yellow, like the no storage or missing construction material warnings) that says "quality bonus is reduced by speed", and let the player click it to see the affected entity.Only generate the warning once for a given entity, (and maybe again whenever something increases the penalty). That way, if we're aware of the situation and want to keep it as is, we don't get bombarded with warnings like for destroyed walls on Nauvis (cough, cough).
Alternative suggestions:
Don't show the quality tooltip until the first time the player installs a quality module.Have another tooltip with specifically this information. Show it the first time a quality penalty exists.
When quality is reduced, emphasize the fact in the entity's tooltip. At minimum, if there are one or more quality modules installed, and the quality bonus is reduced to zero, show the zero value, instead of nothing.