No, don't cut any holes in your cab. Just attach the heatsink to the top, inside the cab, and blow air in from the sides using blower fans attached to the top cab right next to the heatsink. Blower fans, unlike regular PC fans, suck air from the big side and blow out one of the narrow sides, on another axis.
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This gets you the absolute minimum wasted vertical space and still get good airflow. If you have a fan mounted on top of the heatsink you not only have an inch for the fan but at least 2-3 inches of space for the fan to suck air. Unless you have a pressure rated fan, the flow will drop very fast as it gets close to a wall.
You can make it stealthy and self-contained but you'll lose maybe 1/3rd of the width of the cab to a compartment for holding the carbon filter, fan, drivers internally light-trapped intake, etc... See Mr. Flux's awesome cab for a totally self-contained and stealthy job.
note, you can have holes in the top of the cab and have external equipment while remaining stealthy if you affix something on top of the cab like a wooden box or storage tote with the bottom removed.