The code has some strange wording about connecting the bonding grid to the electrical ground. First they say not to do it, then they say that it will be "incidentally" connected through the pump and through the pool light conduit. The way I interpret it that means that you shouldn't run a wire between the two, but if the pump happens to connect them then that is alright.
The bonding grid and the electrical ground serve two different purposes. The bonding grid is designed to prevent stray currents from running through the water, while the electrical ground is designed to provide safety in case of a short of one of the hot connectors.
The bonding grid should not be affected by being wired to the electrical ground, but the electrical ground might be compromised by being connected to the bonding grid. The problem is that if there are stray currents in the ground between the main electrical ground and the pool bonding grid those currents might flow through the electrical ground wire, making the electrical ground wire potentially unsafe. It is possible to use a double insulated pump, which doesn't connect the two.
The code is something of a black art in my book. There are a lot of situations that can come up that are difficult to anticipate in advance. The code is trying to anticipate all of those situations. Over the years strange situations come up and they revise the code to attempt to cover them. In some cases they make compromises. I suspect that it would be better if the pump didn't connect the electrical ground to the bonding grid, but making pumps that way might have been deemed impractical so perhaps that is why they allowed them to be connected. Really I have no idea. Code says what it says and inspectors are required to enforce the wording, not the intention behind the wording.
buddywiser, you should have a bonding grid somewhere and the heater and pump should be connected to it. Depending on how your pool was originally installed, I suspect you can find a bonding wire coming out of the ground somewhere in the general area of the pump. If you can't figure that out on your own then you should get a qualified electrician to fix it for you.
There are all kinds of special rules electrical systems around pools. Not all electricians appear to be aware of all of them. As a practical matter, not all pool equipment gets hooked up correctly and by and large people are not harmed. I wouldn't take that risk, and I don't recommend that you take that risk, but some people do.