Nanotech is technology, not magic. Although it can do a lot, there are some limits. The biggest limit will probably be waste heat. The body can usually dump about 100 watts of extra power without sweating. This sounds like a lot, but remember that nanotech motors can be far more powerful than biological ones. A single cell-sized cluster of nanotech motors could use ten watts! (Of course it would immediately overheat and burn out.) When it comes time to choose which medical devices to install in your body, you will be limited by a power budget.
Another limitation is space. Most of us imagine a cell as a bag full of watery stuff, but in fact a cell is quite full of chemicals and structural proteins. A nanobot will need to be carefully designed to avoid disrupting the mechanism, especially if it needs to move around. The good news is that some bacteria can hide in our cells, so we know it can be done.
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