Is it a good idea to organize level specific classes into thier own packages?
Will storing classes into different packages cause any performance loss?
Yes, for your own benefit and others.
No. (It’s very minimal if it does and you shouldn’t worry about it)
Packages have zero impact on performance. They are simply for logical organization and for making the naming of things simple.
Is it best to load all of my 3D models at the very beginning of my game, or should I load them for each level and dispose them as levels change?
Is it the loading and storing that slows down the program, or is it the rendering?
This is for mobile devices.
It depends on what is “slows down the program”. Loading will increase CPU usage, storing will increase RAM allocated.
Loading by level is probably a better idea. If only because you won’t typically need ALL models ALL the time. So if you know for a fact that a given model won’t be used in a level for whatever reason you probably shouldn’t load it.
In many cases this won’t matter as much, unless you have a HIGH number of models and/or a high degree of memory intensive operations happening outside of rendering (Think fancy path-finding and the like).
Is simply not rendering the instance(by clearing the array and then refilling) of the model good enough?