Here is an example of waterjet cut logos in computer cases:
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In a production environment, it would be pretty reasonable to cut the sides of the case, provided you don't have a lot of different points that need piercing (say limit the number of pierces to under 10 or so). Since computer cases cut like butter, the cutting would be on the order of 30 seconds to a few minutes each (or $1-$5) depending on the complexity and number of pierces.
For high production, this is probably a bit too expensive, but for runs of say 10 to 1000 cases, it may be reasonable.
For low volumes (1-10 cases), drawing the artwork and making the tool path and setting up the machine and such add a lot of cost compared to the very quick cutting, which is why a place like the above charges much more money.
Carl