You should try drilling low (under/near the keyhole if an I/O, also an inch or two up from where the transom meets the hull) and around any thru-hull fittings. On an I/O, the transom is 2" (or more) thick, so drilling in an inch - from the inside of the boat - is safe. Sometimes you have to remove some decorative panels or other stuff that may be bolted to the transom on the inside. It wouldn't be a bad idea to check the motor mounts and the stringers (structural members that run the length of the boat under the deck) by drilling, too. If the shavings come out light and dry, you're good and you can fill them with 3M 5200 or something similar. If the shavings come out dark and/or wet, you have bigger issues to deal with...
Agree that the hammer test is fairly worthless.
A 1990 boat is 27 years old at this point, so finding some rot would not be unexpected. Hope you get good news!