To the first point, it seems that most of the disruption of trade was focused on military trade and was heavily focused on actually destroying/controlling production centers rather than destroying jumpships - though I do not have my books on hand so will have to verify/annul that part later.
How did the Great Houses traditionally make up shortages of military JumpShips? By conscripting civilian JumpShips which not only disrupts trade but turns the civilian Jumpships into military targets.
And while the Blakists did focus their efforts on military targets, they didn't neglect civilian targets as this quote from Jihad Final Reckoning (p82) attests.
Interstellar production of transportation, communications, luxuries, and even basic necessities were smashed on a great many worlds, sometimes by accident but just as often as part of a deliberate strategy to undermine the anti-Blakist forces by burdening them with a further-diminished civil support. When you are facing collapsing infrastructure, millions of deaths and probably millions more displaced citizens, it becomes a tough call to choose between pursuing the villains who created the situation, or saving as many failing systems as you can to minimize the losses.
And that only accounts for the JumpShips destroyed by the Word of Blake. One cannot discount the large numbers of JumpShips of both Blakist and non-Blakist origin destroyed by other IS powers and various Clans (ex: Black Dragons destroyed numerous Nova Cat JumpShips, AFFS destroying CCAF and Taurian JumpShips and vice versa, Regulan targeting all Blakist assets including JumpShips, etc).
I do feel the need to mention that the destruction of warship/jumpship yards doesn't mean that jumpships were specifically targeted - each of the three shipyards you mention as being destroyed were very specifically able to build warships, making them fall into the military target category.
You missed my point entirely. With the destruction of several key shipyards and several other shipyards being heavily damaged/crippled over the course of the Jihad, the ability of the Great Houses to replace JumpShips lost during the Jihad was severely crippled. End result: fewer JumpShips at the end of the Jihad than there would have been if those shipyards hadn't been destroyed/heavily damaged/crippled.
To the second, that convoy was a Raven convoy, a small number of Shark jumpships were included. It was also the third such convoy, and though it was the stated to be the largest (and last) of the three, the mention of it being nearly 100 or more than 100 jumpships (with a star of warships) leaves a large range of possibilities for the other two Raven convoys. The other clan convoys didn't get much mention, but almost all of them had quite a year or two more time to move than the Ravens as they were the snakes' first real target. (Edit: oops, I keep forgetting that the Sharks lost a large convoy in route to the OZs to the Burrocks)
So where are all these JumpShips? JFS (p113) clearly implies the Clans are suffering from a shortage of JumpShips which they need to rebuild their infrastructure.
Given the needs of the Clans to rebuild their infrastructure it can be safely assumed that their naval construction—like that of the Inner Sphere—will be devoted to JumpShips rather than WarShips for the foreseeable future.
This quote (JFS, p113) clearly implies that the Falcons are suffering from a shortage of JumpShips.
...Olivetti Weapons has been starved of resources to build its ’Mechs by ongoing rebellions and a lack of JumpShips.