Assalamou Alaikoum Ahmad,
The GDS files retains the physical information only. All the logical
information, like a pin name would not be translated into your GDS.
If you are using Calibre for example, usually we put a label a in
'pin' purpose on the 'drawing' purpose of the same metal. This is not
a rule, this is what you may define in your Calibre deck. So to answer
your 2nd question, the LVS does decide upon what you have written in
your deck, i.e which layer do you attach to what metal. In Calibre one
could attach a text layer on a metal and then define a port on that
layer. All this is very detailed in Calibre docs.