You're not the first one I've heard mention this issue, so it's clearly not an isolated incident.
I can't comment on Switch use because I haven't tried it with my Switch yet, still rocking the Wii/Wii U mode firmware, but from what I've heard it's not an issue specific to the Switch support, it can happen on other devices too. Haven't had any issues with lag when using it on my PC or on Wii/Wii U games myself.
That could very well be it, the Switch isn't exactly known for good wireless connectivity and it's not an issue limited to the JoyCons as the integrated wifi gets poor signal as well.