You won't see any Victory or Liberty Ships in 1939 or 1940, as they didn't exist at that time. The game will not spawn them until the period when they existed historically, because of the availability date set in the .cfg file under each nation's roster (only the US has the Victory, and the US and UK have the Liberty). If you would rather see the vessels spawn early in the war despite historical reality, you can open the LL.cfg and VV.cfg files in the UK and US roster folders and change the appearance date. For example, for the US Liberty file:
AppearanceDate=19410927
to
AppearanceDate=19380101
Of course, in the stock campaign, you still won't see it in convoys, as those entries are specific and not randomly spawned. In GW 1.1a and NYGM, I am sure that almost all entries are specific and not generic.
As for troopships, they are far more rare and will almost never appear outside of a convoy (at least in my experience). Sometimes, I have seen a single Troop Transport or Passenger Liner in convoy's leaving the UK, but not often. Once, near the Eastern Seaboard, I saw a large convoy with multiple transports (although I was only able to damage one before being sunk
). I would assume that as the war progresses, you will see more of them if you approach more larger convoys.
In regards to mods and transports, there are five new transports currently available: Sergbuto's Transport (NPTR), Combatplanes Fast Transport, Chris911's Large Old Liner, my Chatham Troop Transport (misspelled by Hans Solo as Catham), and UBOAT234's Cunard Liner. These vessel are in the following mod packs (to my knowledge:
NYGM - NPTR, Large Old Liner.
GW 1.1 - NPTR, Large Old Liner.
AOD - NPTR, maybe Large Old Liner.
War Ace Campaign - NPTR, Cunard Liner, Chatham.
I don't think any of these packs have the transport from Combatplanes.