In-game bonuses are effects that affect player ships by either making modules/backwalls of a certain type cheaper or giving them a slight bonus in some other aspect.
Currently there are two ways to gain bonuses in the game, with some of them being locked to the campaign mode only.
Hereditary bonuses: Hereditary bonuses are effects given to players and NPC factions by the main (first) design on their coat of arms, having more than one decal on the coat of arms does not give multiple bonuses as only the first design counts.
City bonuses: These bonuses are only found in campaign and are unlocked by capturing a city, they do not negate hereditary bonuses.