1) how long will it take to assemble the necessary ships? will corporations willingly leave their boats in places where they could be "requisitioned"? will individual captains, hearing rumors, avoid this draft? (recall when we here in california were having our electric power shortages the first thing governor davis talked about was the state seizing the power company's equipment. the company promptly responded by moving every piece of mobile equipment it could out of state and transferring it all back to its parent company.)
A lot will depend on how much of the total available civilian shipping you're talking about. If the sector has 186 billion tons of shipping, and you only need 500,000 tons of it, that's very different from needing 25% of the available tonnage.
To go to a somewhat older example, note that many passenger liners were placed into service during WW1, WW2, and during the Falklands War. Usually, like with the CRAF aircraft, there's some agreement with the owners already in place that covers some sort of compensation. If an airline contracts to have its planes as part of the civilian reserve, it gets a shot at some lucrative air-freight deals, for instance.
Moving ships out of an entire sector is radically different than driving a few hours to get across a state line, too. There are other options if a government is willing to play hardball -- if Governor Davis had arrested the managers and directors of the power company, and placed the families of all the workers who had removed equipment into "protective custody", I expect that the equipment would have reappeared in short order. He'd have had legal trouble to deal with, and some really upset power-company workers, but he'd have had possession of the equipment. The exact nature of the legal trouble in an analogous situation would depend entirely on how much legal control there is over the requisitioning authority.
The Imperium is a government of men, not laws, after all.
2) how much will this disrupt civilian trade?
Depends on how much excess capacity there is, and on the actual demands of the situation. While some level of overcapacity is just a facet of the way trade works (meeting any unfilled needs, and allowing for the inefficiencies required for maintenance and human nature), it won't get
too dramatic, or economic factors will cut some of it back out. There's also the "There's a war on, you moron!" factor to consider, too; some disruption is expected and accepted.
3) are the ships fit for duty? if (when) they break down, are civilan support systems available to keep these things running? do they have the necessary attributes for the job - maneuver, jump, stealth, comms, endurance, armament, armor?
Depends on how much you're talking about, and what arrangements have been made beforehand. Presumably, there's currently enough civilian support systems to keep them running now, and those facilities can be commandeered to some degree in wartime. Combat losses may cut into the number of ships needing support or facilities to provide support -- your specific rules may give more details. The capabilities will also depend on what's needed, and what's out there; bulk hauling will be easy, but high-speed handling of hazmats might not be so easy to find.
I'd also expect that the Navy has been eyeballing civilian shipping with an eye to what their projected needs might be in case of war -- the CRAF example springs to mind here.
4) just who is crewing these civilian ships? are they competent? are they loyal? are any of them sleeper agents? if you give them a cargo worth 100 MCr and tell them to jump to a certain location, will they actually go there?
A lot depends on the nature of what you're going to need them to do. If the job is "Deliver a platoon of assault troopers with all their gear to World X, and drop them off at the navy base there", I'm fairly sure they won't try to run off with that cargo.
There's also the often-neglected factor of the loyalties and other ties that crews may have to their nation-states, too.
I'd rarely expect to see impressed shipping on the bleeding edge of the front line; it's doubtful that the crews would know what they're doing, or be well enough equipped to handle the situation. Instead, they'd get to do the non-glamorous things, like haul containers of ration packs or tents. In the rare cases when they would be doing something like running supplies into hostile areas, they'll either be well-compensated, or given some other strong motivator to get the job done -- maybe the ship's captain has a daughter who is depending on a noble's permission to marry her true love, and the noble will only give that permission if the captain makes sure that the huscarles get this shipment of ammunition.
