I've never owned that amp so the thoughts I express here might me incorrect but I'm thinking more like 8" to 12" clearance for cooling.
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No problem at all with your clearance. The amp is well designed for cooling. Not only does it have a fan as Brf mentions, the tubes are mounted horizontally and the amp is vented on the bottom, as well as the top. The air flows through the amp and the tubes are right in the middle. Very similar to what a good computer case and power supply does for cooling. It makes perfect sense but the drawback is that it doesnt look like most other tube amps. Most people like the tubes where they can see them.
I'm thinking of putting my ARC VT 100iii in a rack, which would leave about three inches clearance above. It runs pretty warm. Any thoughts or experience about whether that would allow sufficient cooling?
3" seems pretty close to me even with a fan.
Why not contact ARC and ask them.
Phone # 763-577-9700