The way I've seen it explained, orders were placed for blocks of boats and the numbers assigned to each. There was no particular concern with consecutive numbering, as was done with American boats until the Seawolf's and that abortive effort to start over (at 21). In both countries, numbers were assigned before construction started, so if a U-boat was blown up in a bombing raid before it was completed, or construction was simply stopped for some reason, that number would never appear as active. We had the same thing in the U.S. around the end of the war, with quite a few boats cancelled partially completed, resulting in skipped hull numbers, mostly in the 400s.

It has also been suggested that the U-boats were assigned wildly varying blocks of numbers for intelligence reasons. That is, to make it harder for the Allies to figure out how many boats the Germans actually had. This story is generally thought apocryphal, though there certainly were some very wide gaps.

In the U.S., small blocks of numbers were assigned to particular shipyards, so that, say SS-212 through SS-218 would be built at Electric Boat, and SS-219 through SS-223 at Portsmouth, and so on (I really have no idea if those particular boats were actually allotted in that fashion and it's too late to go look, though I'm fairly sure about SS-212 and I know SS-224 was EB built). I believe the Germans employed a similar system.

J.T. McDaniel