Hi Simon,
I've had a look through my photos but unfortunately I can't tell if they covered up the aft container hatch. Annoyingly there are crewmen standing over this part of the deck and I can't see it properly. But I would guess you are right that the very late VIICs and VIIC/41s such as U 250 were buildwith no aft container hatch. There was no opportunity to change to spare torpedoes due to Allied air cover so this makes sense. Sorry I can't provide evidence for you.
In regard to the plank width I have looked at this for the first time tonight for the planked deck. You are right, there are differences. All the early boats with the planked deck had the same number of planks as the slotted deck (as mentioned my estimate is 100mm for the width of both the plank plus the space between). But the very late VIICs and VIIC/41s such as U 250 have fewer planks (with the planks themselves being wider). Here are some quick figures I noted down (these are the number of planks across the deck at various locations) -
Around the position where the 88mm would be - slotted (38 planks); early planked (38 planks); late planked (32 planks).
Around the ammo hatch directly behind the tower - slotted (26 planks); early planked (26 planks); late planked (22 planks).
Around the bollards on front deck - slotted (20 planks); early planked (20 planks); late planked (16 planks).
Around tripods on aft deck - slotted (20 planks); early planked (? planks); late planked (18 planks).
This isn't a proper study but enough to think that there were at least two different plank widths on planked decks. The first would be the same number of planks as on the slotted deck. The second would be on much later boats such as U 250 which had wider planks (and so fewer planks were needed).
At a very quick guess I'm thinking that on the very late boats such as U 250 the width of both the plank and the space between the plank added up to 120mm (since 38 / 32 = nearly 1.2). I haven't really looked at what the breakdown would be, perhaps 100mm for the plank and 20mm for the space (?) but I haven't tried to estimate this properly. However, your estimate of 100mm and 10mm might well be right and better than my own quick look at the matter.
Cheers,
Dougie