I was curious about this question and I did some research on the past.
I also did some live tests using a time machine.
Here is what I learned:
1) If the movement is laterally / horizontal coupled (Omega 321/861/1861, Zenith El Primero etc.) there are consequences:
The balance amplitude will drop, meaning that the watch will run fast.
The drop amount depends on the overall state of the movement (new or recently maintained will drop less).
There is a potential wear.
2) Vertically coupled (JLC 758, IWC 89361, etc.) there are no consequences.
About the misaligned seconds hand, I never hear anything about and I consider this as another watch "myth".
That's what I know but I would like to hear from the experts.
Cheers,
Nilo