I typically tend to keep my rhtymic and stereo effects separated into one bus.
But, i also have busing going on inside my of my channels before i hit the main buss effects.
in all honesty, it depends on the sound you're working with. If you've managed to get a good mix on the sound and you're ok with making it more concrete, then go ahead and bounce it with what ever effects you have on it.
But you have to understand that those effects will be there, at the mix that you placed them for ever and until you decide to rebounce or change.
I use fade ins and outs to make sure my audio clip doesn't clip and pop.
When you bounce audio, you have to consider the sound tails and allow for the render to capture that audio, unless you're dealing with ableton. Ableton handles the tails a little differently.
Just see what works man, you can always go back and change things if you keep multiple files and are unsure of what to do.