Well Point Pleasant was even worse for the low numbered platforms. My guess is the up ECS needing low numbers went to 5 and 6 and departed Down Slow. Slightly off topic am I right that low numbered platforms needing Wimbledon Park sometimes went to Hampton Court to reverse and then back to the depot?
As far as I was concerned one tried to keep the plan as simple as possible. Minimum conflicting (crossing) moves etc, so as to minimise any potential disruption. Empties out of Wimbledon Depot via East Putney would normally be for Windsor line services starting at Waterloo (Windsor side). In bound to Wimbledon Depot via East Putney could be off Windsor line services or certain main line services. In the case of the latter these would where possible be planned to arrive Waterloo in the plat 12-15 sort of area (I am talking pre Waterloo International here, although the basic principles didn't change after then), so their outbound empty journeys had straight forward access to the Down Windsor Lines.
Trains starting on the Mainline suburban side at Waterloo, if formed of empties from Wimbledon Depot, had a couple of preferred routes. The first was from No 1 siding in the depot (alongside the Up Slow line at Wimbledon station end), from where an empty could depart and then run up and over the flyover, so was positioned on the Up slow from the off, and the other exit from this siding was at the Staff Halt out on to the Up Fast. In this instance any such train could then (if required) cross to the Up Slow at that same point outside the depot (via a ladder from UF to US) or alternatively at London end of Vauxhall. In addition there was a third exit at the Earlsfield end of the depot, out on to the Up Fast again.
Inbound empties to depot from Waterloo main side, would generally be planned to run Down Fast from Waterloo (or Down slow to Vauxhall then out to DF) and enter the depot at the staff halt, but most such moves were (in my time) restricted to late evening as a rule, as crossing the Up Fast outside the depot could prove difficult to plan. Hence main line trains requiring the depot after the morning peak generally went Down Windsor and via East Putney, as mentioned above (plat 12-15).
Yes, your last point is quite correct. When no other paths were available to get in to the depot, certain trains left Waterloo and ran to Hampton Court, and/or Chessington to turn back, entering the depot off the Up slow just London side of Wimbledon station.
