In Civilization, "bonus resources" are tiles that contain unusual natural resources, like gold ore, fish, wheat, and so forth. In ACKS, these might raise the Land Value of a given hex. In the Simple Domains subsystem, this turns into an adjustment to monthly income and taxes. I assume here that a resource is limited to a single six-mile hex, and that it boosts that hex's production from an average roll of 6. Marginal resources like bog iron raise it by 1 point, average resource sources like a typical iron mine raise it by 2 points, and excellent resources like a gold mine raise it by 3 points.
Given the population density assumptions of Simple Domains, each point of LV in a hex is worth about 400gp/mo of domain income. If you're a vassal, you owe about 100gp/mo of that in taxes, and keep the remaining 300gp/mo. So in the best case, as an independent ruler with control over a +3 resource hex, you're earning an extra 1.2kgp/mo. In the worst case, as a vassal with control over a +1 resource hex, you're earning an extra 0.3kgp/mo and paying an extra 0.1kgp/mo in tax.
In the interest of simplicity, keeping track of +1 resources probably isn't worthwhile; about 22% of hexes as rolled will have +1 land value, with a counterbalancing number of -1 LV hexes, so in total around 70% of hexes fall into this range. About 10% of hexes have a +2 resource (and 10% have a -2 penalty), and only about 4% have a +3 resource (and another 4% have a -3 penalty). I'm more than willing to assume that the majority of the world's penalty hexes are unsettled, to not keep track of them in domain play (until someone decides to go settle a desert...). Even just having 15% of hexes be bonus hexes might be annoying to track; that would mean that an average 16-hex county would have 2-3, which leads to increased paperwork. Just tracking +3 hexes might be best; an average county probably won't have one. On the other hand, the gains for a count from one +3 hex are pretty marginal; given that his income is around 50kgp/mo, 1.2kgp/mo extra might not be worth going to war over. Maybe lines or clusters of +2 or +3 hexes in (for example) prime floodplains farmland would make these worthwhile objectives for warfare? But then you're back to the tracking problem. Ugh. Maybe tying land value directly to hex/terrain type, since that's state that is already tracked? Desert and glacier at -3, floodplains at +3, and then infrastructure projects (clearing forest, irrigation) can change the type of the hex? This is Civ's solution before even adding bonus resources...
At the end of the day, the correct solution for Simple Domains is almost certainly a per-domain modification to average land value - this immutable domain is Rich, with an average land value of 7 instead of 6, and produces an extra 400gp/mo per hex (or 300 for you and 100 for your liege, if a vassal). So a Rich Vassal County has 16 hexes, earns an extra 4.8kgp/mo, and pays an extra 1.6kgp/mo in taxes. That's enough money to be worth keeping track of (a >10% increase in income), with little enough paperwork. Boom, done.
Probabilistically, a +2 or +3 average land value would be quite rare for any domain larger than a barony, so I probably only need to worry about having Rich (+1 LV) and Poor (-1 LV) modifiers.