Eh, capacitors go bad, it happens. Replace the capacitor and the system should work. That said, other hardware could have been damaged when it blew. The risk to hardware was when it blew, running it after it has been repaired is low risk. A better question might be, are there other capacitors like that and are they cheap capacitors? Are others likely to go? Some TV repair guys replace all the capacitors when they replace one, they figure if they are going through the trouble they might as well not do it a 2nd time. Mobo's are a little easier to access than TV circuit boards.
I would think the risk to GPU and M.2 is relatively low. GPU draws most of it's power from the power supply, and while M.2 is relatively new, I haven't heard anyone say their's went bad. It's the CPU that is most likely to be affected. Since you were already considering a new CPU and mobo...
Personally I'd try to fix it. It's likely a $3 fix if you know how to solder. If I were working on someone else's computer, I'd tell them to replace the motherboard. That's because I want them to have a 100% positive experience, and replacing the motherboard is a sure fix; while replacing the capacitor is not guaranteed.