I took the used intercooler I want to put in my car to a shop to have it tested and cleaned. When I got it today I found out they had painted it in a silver colour. While I am annoyed at that, I was wondering what is the impact on the effectiveness of said intercooler after being attacked by the Krylon Monster

 

Black may allow the heat to slightly dissipate quicker, other than that no difference. There are thermal dispersement ceramic coatings that do make a significant difference. Most people appreciate a shop that paints up a part they worked on but the paint is only cosmetic and will not affect cooling performance.

 

Picture showing one of the ports after being painted. Note tape remains
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What is sad is u probably paid for that . I bet there is a supplies line on ur receipt . I had an aluminum driveshaft shortened and paid 12 bucks for a crappy black spray job

 

The difference may be negligible but I still would rather an intercooler which is exposed fully to the environment and not insulated with any superficial layer. You want the engine insulated, the exhaust insulated, yes as much as possible. But between the turbo and engine there should just be aluminum and no insulating done at all, no wrap, no coating, no painting on any of the items between turbo and engine intake side, you want the heat to escape as often as possible along the way.

Here is a random google search showing general thoughts. Google is not always right and the result may be exacerbated... nevertheless paint is an insulator and does not belong anywhere in the plumbing of intercooler or on the intercooler.
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Yes, the colour is going to be irrelevant. Most of the heat rejected by an intercooler is via convection. Colour only matters for radiation heat transfer and that would account for less than 1% of the intercooler heat rejection.

Yes, almost any layer you add to the aluminium will reduce the heat transfer. One exception might be a highly textured layer that increased the surface area significantly.