For polymictic and dimictic lakes, yes. Pipes near the bottom of polymictic lakes work very well due to the water quality being generally the same throughout the water column. This also allows the pipes to stay under water if the water levels drop. For dimictic lakes it’s also better to have the pipe near the bottom, though you’ll need to watch out for the water quality in the hypolimnion. It could deteriorate over time.
For meromictic lakes it’s better to have the pipe in the upper portion of the lake, or the mixolimnion, due to the poor water quality of meromictic lakes. Most of the contaminants will be near the bottom, though the upper levels aren’t much better.