Again, I I noted, it doesn't HAVE to be a huge fraction, nor does it have to be to the exclusion of Harris' beloved "dehousing". Weather over Germany was frequently bad enough to cancel missions, it is a simple matter to alter the bomb load to strike the ports on these nights. As Carl pointed out the range is such that medium bombers can easily reach the targets with a good bomb load. THe RAF could even combine mediums with a strong fighter escort (the French ports are close enough, especially Brest, to allow Fighter Command enough loiter time to cover the strikes ALL THE WAY IN AND OUT).
The Germans understood this, that is why they took the insane risk of the Channel Dash. Better to maybe lose the ships than leave them where you WILL lose them.
I thought these ships were heading to St. Nazaire, not Brest.
To you point about fighter coverage, all the stuff happened IOTL, and it was very resource intensive for the RAF compared to the damage done. I am not saying the ships last forever, or that they are not damaged. Or that at some point the Nazi are not going to make a use it or lose it choice sortie in the Atlantic. Or some channel dash ITTL. You are overstating the effectiveness of the RAF by not putting enough weight on similar missions from OTL.
It is just when you come at it from the Luftwaffe bomber defense command, you see how valuable it is. IOTL, the Luftwaffe struggled to contained the British bomber offensive and meet other Luftwaffe needs such as Russia or the Med basin. From the perspective of the Luftwaffe generals, this bomber command attacks were a godsend each time they happened. Instead of defending many German cities, you had a fairly obvious target. i.e. The bombers headed in the general of a French Atlantic port were not going to gut some French city. Nor are there a lot of other German high priority targets in the area. So when Germans picked a raid towards these French ports, there is one target to defend compared to a bomber wave heading towards German which could be dozen or hundreds of important targets. Deploying the German fighters is a order of magnitude easier to do. And it is much easier to deploy the flak.
The point is that in 1941, the German fighters have to interact daily with UK fighters. It is better to do this at place favorable to the Luftwaffe, and these ports were about as favorable as it got.
And we then get the damage side. The Bomber command did hit and even more commonly came close to hitting important war targets on raids on Germany. Here, the war target is not really that important from the perspective of the Luftwaffe or the Heer.
So we end up with a double win from OTL perspective. Better defensive situation for the Luftwaffe, and when it fails, less real damage to the German war effort. Again, I don't think it is huge or a war winner, but take a few percent off the western fighter command losses, it helps. Maybe add a few % to the UK losses since the Spitfires are not attacking near to the UK (Belgium for example) and making much longer trips where if nothing else, mechanical losses add up. Then we get some buff to the German war effort, but off the top of my head, I can't list the major losses to Germany from Bomber command in late 1941.