Switching BLE on/off and get additional 29KB into heap

Yes, you could calculate the vars - but as I said above it'll mess up saving/loading if there isn't a fixed number of vars.

One more question could we do something like Bluetooth = nothing;

This is what @Wilberforce suggested. If you had saved code there are still ways to keep access to that object so it can be used - but I guess if you're destroying any saved code when you update it's ok. On boot you'd need to jsvObjectSetChild(execInfo.root,"Bluetooth",0) - it can still be worked around though.

Personally I'd recommend modifying each function - that way the user actually gets a Bluetooth not enabled message.