Why is Glycerol 3-phosphate named in such way? Shouldn't it be named as Glycerol 1-phosphate by proper IUPAC- nomenclature?
You're right, according to standard rules of nomenclature it would be called glycerol 1-phosphate. It comes back to the outdated D/L configuration nomenclature. A more thorough explanation is quoted below.
When the R/S system (sequence rule) is applied, substitution of one of the primary hydroxyl groups often leads to changes in the configurational prefix, thus obscuring chemical and biogenetical relationships; it is generally inapplicable to the steric description of such mixtures as occur in triacy1glycerols isolated from natural sources. The stereospecific numbering of glycerol and its derivatives as proposed by Hirschmann , described above and in 1, avoids these difficulties; it has proved useful and is widely accepted.