Forgive me if I am telling you something you already know, but it sounds like you could benefit from a little tutorial on Engine Cooling 101.
I am not personally familiar with your engine. But I assume it is what we call "fresh water cooled".* This means that the engine has a closed cooling system, like your automobile, which circulates coolant (usually antifreeze) around the engine block to take away the residual heat from combustion. This is the "fresh water" part of your cooling system (again, usually using antifreeze instead of water).
The coolant is then itself cooled by passing it through tubes in the heat exchanger. The heat exchanger uses "raw" water taken from outside the boat, which is also pumped through the heat exchanger, but in parallel conduits to those through which the "fresh" side of the system passes. In other words, the "fresh" and "raw" water passing through the heat exchanger do not mix in any way.
As they both pass through the heat exchanger, the "raw" water sucks the heat away from the "fresh" coolant system. The cooled "fresh" fluid then gets pumped back to the engine block to grab more heat from it. The now hot "raw" water gets pumped out of the boat and discharged out the tail pipe with the exhaust gases from combustion.
Then got to thinking- could there be seawater in the oil? I mean, where did the exhaust and cooling water go while it was running??
In your case, when you neglected to open the raw water thru-hull, the heat exchanging process never occurred. So there was never any "cooling water" that went anywhere. Your "fresh" cooling system (antifreeze) simply continuously recirculated in the closed system as it normally does. The exhaust gases from combustion would have discharged out the tailpipe, again as they normally do (albeit more loudly, for sure, since the waterlift muffler system uses the raw water to mix with the exhaust and thereby both cool and muffle it.)
While it's not good to run the engine with the intake thru-hull closed, my hunch is that your operation times were very brief and you probably did not overheat the engine. The run over to your new slip suggests things are okay. But do take a good look at your engine oil. If it looks like you have any milky water in it, you'll need to inspect further and maybe get some expert help.
*There is another, less common, form of cooling called "raw water cooled". In this system, there is no heat exchanger and no anti-freeze is used. Instead, raw water is taken in from outside the boat, pumped through the veins in the engine block, then mixed with the exhaust gases and discharged overboard.