That would actually make a lot of sense. I pulled the original roof rack off to put my pioneer rack on and there were zero seals or sealant around the bolts. Did pull the ECU plugs and dry them out? Or let them dry over time?
The roof rack is meant to have a rectangular piece of rubber with two holes for the bolts to go through, so when you do up the bolts, it should make a watertight seal, assuming there's no or only a little rust.
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If the rubber is not there, then I'd almost guarantee that water is getting in there.
Mine has a lot of rust, and that has made it hard to get it fully watertight, so I still get some water in.
I couldn't find the actual rubber parts available, I ended up using black selastic - a silicone compound, which probably isn't the best way, as it will make it difficult if I ever need to remove the roof racks.
My car has a rubber floor interior, so no carpet to worry about.
And when liquid did get in there and onto the ECU, by the time I got back to the car, the hazard lights being on all day had flattened the battery.
I jump started it, without drying any component, and it started.
One other time, a few weeks later, I did see the hazards come on, again after rain.
I find parking uphill reduces the issues, as I guess any leaks drain towards the back of the car.

If you hear any sloshing of water, and its not in the doors, you may want to check the drain plugs that are in the rear wheel wells, on the front side.
After very heavy rain, I heard it sloshing around, then happened to notice those black drain plugs, and several litres came out of it.

Good luck with yours.