Why can heart virus, poision and diseases still kill Goku?

[Polyphase Avatron]

If you want to apply science to various scenes like that, you have to also take into account that it makes absolutely no sense for the damage to become greater the farther away from the impact it is. So if the damage can somehow threaten the universe but leave the Earth right below them unharmed, it's hardly so much of a stretch to say it would leave Goku's bones unharmed too.

Your right, that might be a bad example. Then how about him punching through Kaiou's planet?

Perhaps, but the answer could be related to something known as the Fallacy of Division - i.e., the assumption that any property that holds true for the whole of an object necessarily holds true for any given division of it. So while Goku's body as a composite may be ridiculously tough, that doesn't necessarily apply to his individual cells or tissues taken in isolation. For example Dr. Gero's robot probe was able to pierce the skin and extract DNA from all of the Z-senshi, the Saiyans, Freeza and King Cold without any exceptional difficulty.