To answer my own question, the solution was to remove the slot0 -> slot3 definitions from the device tree - that way, the cape manager runs, but does not invoke the i2c driver to search for EEPROMs on the capes. This may also speed up the boot, as it won't wait for the timeouts from each of the (empty) slots. It may even be worthwhile to remove the "extra" slot definitions if you know that your application will always have only N (N<4) capes installed...
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