How can I tell whether my baking recipe has enough acid to activate the baking soda?

Both brown sugar and molasses are slightly acidic, you are right that reducing them reduces the acidity. However you need to consider that baking soda's purpose is a leavening agent, not to neutralize acid, so if you take some baking soda away you need to replace it with baking powder or you won't have enough leavening agent.

I can think of 2 ways to go about this, there's the lab science way and the simple way.

The lab science way would be to dissolve the amount of sugar and molasses you plan to use into some water, and then add small amounts of baking soda to the mix until you have a neutral ph. You can measure acidity with an expensive electronic meter or by using paper strips. However much baking soda you add to get a neutral PH is the right amount. You'll need to measure things exactly for this to work, then replace the balance of the baking soda with baking powder to have the right leavening.

The simpler way is to look at proportions and adjust as a ratio. If 1 tsp of baking soda is good for 1 cup of brown sugar and 1/2 cup of molasses then reducing the brown sugar and molasses by half means you need to reduce the baking soda by half. I personally would weight the molasses and brown sugar rather than using volume measurements, and adjust proportionally using weight of both added together. IF you reduce the combined weight or both by 25% you would reduce the baking soda by 25% and replace it with baking powder. This may need some tweaking, but it will get you pretty close. Be sure to take notes so you remember what you did.