A seaplane rating is all about surface operations; instrument flying is all about flight above the surface.
Your instrument rating is for airplanes, in this case; it applies as others have said, equally to seaplanes or land planes; it applies to the category (airplane), not the class (single engine sea, for example).
The area to which you're approaching while operating under IFR in a seaplane may or may not have an instrument approach, and you may or may not need one; you don't need a destination to be IMC, or to have an approach, to file there, as you can file to any point in the NAS system (including a lat/long, if you like). You may intend only to file to VFR on top...a properly equipped and certified aircraft may certainly fly IFR, even if it's floats only.
A lot of float aircraft are amphibs, and capable of shootin approaches to hard surfced runways, or as another poster pointed out, flying to a runway and circling to water. Likewise, approaches are available to water.