For sure. Both from third parties and Nintendo.
Acce$$ories are big money-makers, so this definitely won't be ignored.
Hard cases and soft cases will be made for transporting the unit easily with joycons attached or detached. That is certain.
But to get a convenient case to properly protect the unit on all sides while it is being used with joycon(s) detached or attached might be more involved. A case that doesn't need to be removed or put back on when the Switch is in its different configurations.
detachable velcro or magnet skin
I suppose they could work on an detachable velcro or magnetic system to cater to the joycons being removed. It's very possible and not hard to do well with a little thought. Both the main Switch unit and the joycons could have 'extra skin' to wrap around themselves when the joycons are removed. So there is skin around the LEFT and RIGHT grooves of the main unit and there is extra skin wrapping around the (removed) joycons to protect the side of the joycon that slides into the groove on the main unit.
It's all possible.
But more concerning to me is that the masses will just consider the Switch the modern Atari Lynx / Virtual Boy when out-and-about in a portable situation.