So what you're saying is that...no matter how much Shield Regen you have...you still have to wait the 3s before it starts to regen?
No. Shield Regen means a ships will regenerate at the given rate regardless of combat state. You can look at the Shield detailed description. It will tell you the amount and rate of regeneration. For example my Mk XI Jem'hadar armor has +7.6 / 4 second shield regeneration. It does that regardless of my combat status.