Like all things boating it's largely a matter of choice. And if you're shopping the lower end of the budget scale and older boats you won't have as many choices. Better to look for a well maintained boat than shop a specific characteristic such as N/A vs T or TA.
My opinion, not fact, just opinion is that turbos on well maintained and properly operated engines last a long time without problems. But when they fail it can be $$$. Add aftercooling and now you are adding maintenance costs to maintain the cooling system. Failure to maintain the system is inviting huge costs.
My experience with N/A vs TA has been mostly on CATs from the mid 60's to the mid 80's vintage. You asked about low speed performance maneuvers and docking. I don't find a lot of difference because the Turbos haven't produced enough boost to matter if they have produced any boost at all. Before turbo boost kicks in the same block and pistons are going to produce the same, or very similar, toruqe and HP. I'm speaking about older iron here, the newer stuff may be considerably different.
When I say a properly operated T or TA engine I'm speaking of running it hard enough to get the turbos working well. If you don't, depending upon the engine, you may have issues including oil build up in the turbo, carbon build up as well. And with Aftercoolers all of that crud gumming up the aftercooler. I'm not talking about running it at max power, that just wears things out quickly.
Something I'm learning about mid 80's "trawlers" is that they can be both underpowered and overpowered at the same time.
Two examples.
#1 My last boat a Californian 42 LRC with twin CAT 3208 N/As. 210 HP each, 420 HP total. It cruises very nicely at 1400 RPM, smooth, quiet, acceptably low fuel burn. But I've been warned that running that RPM is too low and the engines may suffer. So I ran her at 1600 RPM. Noisier, higher fuel burn for only about 1 kt gain in speed. Going any higher RPM was a wast of $$$ unless I needed the speed. I did run her at about 2000 RPM for a brief period each day to clean things out. At max RPM she was making 12 kts, a huge wake and burning a LOT OF FUEL. So, at 1400 RPM she wasn't working hard enough, she was overpowered. At max RPM she was working her guts out, stern squatted, big wake and not able to climb out of the hole.
#2 My current boat a West Bay 4500 with twin Cummins 6BT. 210 HP each, 420 HP total. Running her at 1400 she is sweet as can be. Very smooth, very quiet, very small wake. I have been advised that that will not get the turbos boosting and cause problems. Run her harder, 1600 min, 1800 better. Well now the same thing happens as with the Californian. Squatting, big wake. At max RPM not climbing out of the hole and burining too much fuel. Same problem, both overpowered and underpowered.
A very long winded opinion of saying if you're shopping engines shop the boat performance and your desired operating characteristics as well. If you wanna go slow buy a boat designed and powered to go slow. If you wanna go fast buy a fast boat. A sorta fast hull with not quite the right HP will present challenges. Or, buy the boat you like and learn to live with performance constraints.