My recollection, for what it's worth, is that Hooton had 7 platform faces in the early BR period.
I think the fast lines (next to the station building) were 2/3, the slow lines were 4/5, and platforms 6/7 (loops) were for the West Kirby line and parcels.
P1 was a south-facing bay on the opposite side of P2, used mainly for Helsby shuttles.
The layout was remodelled/shrunk in 1969 with the slow lines lifted south of Hooton to Ledsham Jn, and the fast lines north of Hooton to Rock Ferry, hence the dog-leg south of the station.
The up fast became a headshunt for reversing freight trains between the Chester and Helsby lines (mainly to Stanlow).
The down fast was truncated as a south-facing bay (now P1).
So I think that marked the point when platforms were renumbered.
It's a great pity that the old up fast can't be reinstated as the main southbound platform today.
It has a decent canopy and feels like a proper station.
It would also have made for a simpler new footbridge as one of the spans would not have been needed (too late now!).
This site has some interesting photos, showing the old numbering.
http://www.disused-stations.org.uk/h/hooton/