What? I have Ventura 13.5 on intel macbook, I was able to install Bitcoin Core v.25.0.0, it works no problem. I don't know about the system upgrade process, this indeed sometimes brakes some stuff like you say e.g. "disappear" app shortcuts from the dock but I highly doubt they specifically target Bitcoin Core.
I think there's a difference on how you install it.
I have seen Bitcoin Core simply disappear from macOS. Not sure what happened, but it was all gone. This was using the "normal" installer.
When I tried simply downloading the console app, it stayed fine.
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