The "turbocharged" EMD's actually use an over-running clutch. Below Run 6, they are in part engine driven. Run 6 to Run 8, they are free-wheeling turbos. If an EMD is expected to be used mostly in low throttle ranges (most switchers and branch units), then the roots blown engines are more efficient (fuel and maintenance). Road units that will spend a lot of time in high throttles are better if turboed.
Some turbos do have overheating problems. ALCO switched from air cooled to water cooled turbos in the middle of the 244 powered production. This can be usually spotted from lengthwise stacks on air cooled units, crosswise on water cooled (new or retrofitted).