20 years of playing this game and I don't remember this ever happening to me as the defender. It would be pretty careless to do that anyway as a hooman against the AI.
Embarked units will not necessarily be visible before you attack the town (e.g if there is a Worker hiding in the town, but he is not on a boat, then after all the non-embarked units are dead, the Worker will show as the top unit), but they
will defend it
[EDIT:] if they can!
i.e. all land-units with a D-value >0, even if on a boat in port, will defend against an attack on that town by enemy land-units.
Air-units on a docked Carrier (if set for Air Superiority at least 2 turns earlier, and with "Cancel Orders for friendly/enemy unit" turned off in the Preferences) may defend against Bomber-attacks (per the RNG) — but if the town is captured, they will be destroyed along with the Carrier.
Biq? Don't know what that is and don't see anything remotely looking like it.
The .biq is the ruleset file.
The one for Conquests/Complete is called (predictably enough) "Conquests.biq", and you can find it in the folder
../CivilizationIII/Conquests/
However, you can only
see the details stored in a .biq file, by opening it in the/a Conquests Editor. The standard-issue Firaxis Editor*, which you can find in the same folder, is called
Civ3ConquestsEdit.exe. When you start that program, go to the "Scenario" pull-down menu, choose "Custom Rules", and click through the "Changing the rules may break your game!" warning.
(Don't worry, the Editor automatically names your 'new' .biq as "Untitled.biq" so you can mess about with it to your heart's content, without any danger of over-writing anything vital).
The Untitled.biq -- initially -- contains all the standard Conquests rules and settings -- including the city-lists for each Civilization (Menu: Rules -> Edit -> Civilizations).
*There are also several homebrew Civ3-Editors available on Civfanatics. The most well-curated is probably the one written by
@Quintillus, which allows additional functionality over the Firaxis Editor.