But its not just the invasion fleets, warships and transport fleets have a teeth-to-tail ratio just like the ground troops. For example, IIRC Desert Storm had a 1 fighter to 100 supporting troop ratio which was the chain from the guy sitting in the desert to the AF enlisted loading a pallet of MREs aboard a C-5 on a stateside base. Its one of the more studied and extended supply chain cases in recent history afaik . . . and Kerensky's situation is worse, it would be akin to losing the continental US with all its bases, supply depots (trust me, MREs sit in a central location before being shipped out), and all the transport located in the US.
Most military supplies that move between bases do not travel in military vehicles (or in this case hulls). Sure, MAC moves a lot of supplies around between bases worldwide but its a fraction of the peacetime needs and to keep costs down as much as possible is local sourced. Critical or secure supplies are what travel on military transport, everything else travels on civilian semis, rail and ships. For example, when my unit was preparing to play in the desert all of our vehicles & cargo containers (Conex) were going to be loaded on a train (civilian), railed to a port to be loaded on a ship (civilian), and be offloaded over in the Mid East where I think it would be put on trucks or a train to be moved to a marshalling point nearer the front. Meanwhile we would still be training while the gear was en route, fly over on a airliner with personal gear & weapons to be bused to where we would meet up with our vehicles.
I mean we could have waited for the USN's amphibious carrier to shuttle us over but that would have taken more time . . . and time means lives. Which is why I said what you are talking about is a fleet that meets the SLN's peacetime movement & needs, it does not meet wartime supply or transport needs- because a fleet that large is not economical since most ships & crews would be idle. War changes economic equations. I once heard it described as rushing to produce & gather a bunch of stuff, ship it halfway around the world, and set it on fire. You are telling me that the SLN did not have the ships to move replacements from training centers outside the Hegemony to Kerensky's army- to me this means they were struggling to get replacement equipment and needed supplies like food & ammo since replacment troops are usually pretty high on the logistics pipeline priorities.
Even looking at just the warships . . . alright, write off the 1000 reserve ships that were located in the Hegemony, whatever percentage (15-33%, depends on doctrine) of the active fleet that were in Hegemony yards for refit- only a few were able to escape the Hegemony IIRC, and then you have ships that may have been abandoned as Kerensky consolidated his forces to move. Which is warships- they have higher security standards and would be able to fight their way free of initial encounters.
Now look at transports . . . rather than operating from established supply depots where you have acres of warehouses that gather, store and prepare dropship-sized shipments destined for units on distant but established garrisons that source as much as possible from local sources (food, butt-wipe, water) Kerensky's forces have shifted to a very dispersed supply chain and either need more money to get intermediary shipping or send their ships to the factory source.
To get back to the OP, in wartime civilian transport is seized to augment what is already under control. So yes, I expect quite a few civilian liners that Kerensky turned into troopships went on the Exodus. I would expect these were kept landed to form the initial core of the colonies the SLDF-in-exile formed since they would have provided ready housing to the colonists who were setting up. Any that were not decommissioned to become apartment blocks were IMO likely to be dismantled by Nick, especially after the Wolverine debacle- he had been unable to completely stop the Wolverines from opting out of his experiment, he could absolutely make sure it was much harder for anyone in the future. The only other source would be the Dark Caste, those who were in space that fled Operation Klondike's first encroachment and the early Clans hunted down to force them into Nick's castes. Face it, if you were living in space to avoid the factional war on a planet's surface, a old spaceliner would be better to live in than a cargo ship's limited passenger spaces.