You can also check by trying to tighten the lag bolts that mount the engine to the stringers. If they turn, your wood is rotten. You can also tap with a screwdriver, wrench, or other hard tool and listen for hollow spots. Drilling is still the best method though - even though the stringers are fiberglass encased, water can get in through motor mount bolts and other screws. I did all of this when I bought my Brendella and was lucky that stringers were solid.
I envy your doghouse! I always thought the split design was brilliant. Can still check on the engine without making everyone in the back seat move in order to lift the whole darn thing.