Does a non grounded GFCI meet code?
Installing GFCI protection on a circuit allows you to replace non-grounded receptacles (2 wire) with a grounded receptacle (3 wire) as long as it is marked "No equipment ground" and "GFCI Protected". If you just replace one non-grounded receptacle with a GFCI then it must be marked "No equipment ground". This can be found in the NEC Article 406.4(D)(2). It is used as a means to install grounded receptacles on a non-grounded circuit and not have to rewire an entire dwelling. The GFCI is not a ground but acts as shock protection due to its design.

If most of your dwelling was rerun in PEX then you should insure that you have a at least 10' of water pipe in direct contact with the earth, NEC 250.52(A)(1). 

NEC Article 250.50 requires that every method of grounded available shall be combined to form one Grounding Electrode System. This means that if you only have the water pipe as your grounding electrode, you should as least drive and attach a ground rod supplementary to the water pipe.

Hope this helps to clear some things up.Good luck.