So, I think I've found a good solution for electrical connections between the frame and module. To recap, we need the following connections:

GND, SCK, SDA, SOL (solenoid), 12V (for led strip), 5V (for microcontroller.)

Now, I've decided to add another 6 pins for module location sensing (which decides the module's I²C address). That brings us to a grand total of 15 pins.

Of course, something that will used so often in the frame and module needs to be cheap.

I think I've found the cheapest thing I will. It's ubiquitous, cheap, and the male connector is the circuit board itself.

PCIe. Of course it will need sanding on the module PCBs, but I'm sure that will cost much less than most other connectors would in the end. I'll use the 36-position version (that's PCIe x1).

About module location sensing: I'm not sure what would make sense in an industrial context, but cut-traces (to ground) on the frame PCBs should be enough for me.

If you're worried about currents being too high for the connector: LED grow light strips seem to take around 600mA/m and the PCIe connector I linked is rated for 1.1A. Just to be safe, I'll probably use more than one pin for this, so I should be good on that front.

I've decided on this pin allocation:

I didn't stay that close to the original PCIe allocation in the end.

Edit 2015-04-25: Added UART connections

About connections within the module: I originally planned to have the microcontroller within the bottom bezel of the board. However, it might make more sense to move this to the top - it is shielded from water there anyway, it's closer to the grow LEDs, and I might get away with one circuit board per module! (apart from the hygrometer). I'm probably going to leave out the indicator LED. Instead, whoever performs maintenance on the system will be able to press a button that causes problematic modules to flash their lights, indicating where they are.

If you have any thoughts on this, please post a comment. Thanks!