Do seaplane bases ever have marked "runways" or approach lighting?
Are the landing areas marked by buoys or lights?
In at least one specific instance, Yes.

The seaplanes that operate out of Lake Union, Seattle, have "Advisory Buoys" that help make the many sailboats, kayaks, and motorboats on the lake aware that planes will be arriving or taking off.

The buoys have Pilot Controlled Lighting (PCL) that will turn on yellow flashing lights.  They are typically activated approximately 3 minutes before any departure or arrival.

The buoys do not restrict boat movement; they are advisory only.


I am not aware of any IFR procedures for a seaplane base, but I do not know for sure.