That is a valid concern, but I am not sure it is a foregone conclusion that the electronics will in fact be less reliable than the acres of boards and high parts counts in old games nor harder to service in the future.
Sure, it is a bit more tedious to probe and do repairs on SMT boards, but definitely NOT impossible for a hobbyist with the right tools and a bit of practice.
The CGC hardware isn't as "proprietary" as it seems either; the entire system operates on a BeagleBoard platform which is open-source, maintains backward-compatibility, and is very widely deployed in industry. It shouldn't be much of a problem in the future for someone like Multimorphic or Rottendog to redesign or emulate the hardware for these games in the same vein as has been done for the old WMS systems. Also, it appears that they retained through-hole packages for the board-level parts most likely to require future replacement (such as driver transistors and electrolytic caps). I am not sure whether the game has any ICs which are proprietary down to the die level (which WOULD be difficult to replace), and imagine any such customized functionality would be implemented with industry-standard programmable chips like microcontrollers or FPGAs (meaning the custom code could be loaded onto a backward-compatible part in the future if needed).