The answer is sort of vague. Some U-boats were in the middle of the ocean and sent a message saying "all OK" and were never heard of again. Others sent a message that indicated distress (or a totally garbled message) and were never heard of again. Others had been under major repair and went out with the plan of returning to port after a "test trip" which often involved a test dive and were never heard of again. Others reported that they were in a certain location and were going to another place and were never heard of again (but some of these were sailing into what are now known to be minefields).

It was important for the Allies to account for U-boats. Partly to keep an idea of how many there were operationally, partly to know how many were operating in a certain area (like the Mediterranean), and partly to analyze how effective Allied tactics were for sinking or damaging U-boats and/or deterring them from launching attacks. Some of these were easy - if a boat was damaged and an Allied destroyer picked up 30 survivors who said that they were from a certain U-boat, then that U-boat would be accounted for sunk (even if the German Navy never knew how, when, or where it was sunk). Others are fairly clear. If there was one U-boat in a 500 mile radius and it reported in a certain location and stated that it was traveling north at 10 Knots and a Liberator bomber reported dropping depth charges on a U-boat 6 hours later at a spot 60 miles north of the reported position and the U-boat was never heard from again, it's pretty likely that that attack resulted in the sinking of that U-boat. Others didn't become obvious for years - say if an Allied destroyer reported dropping depth charges but didn't see any signs of damage but an underwater oilfield ROV finds a wreck 70 years later at that spot and it can be matched to the type and configuration of a U-boat that disappeared, this one becomes pretty obvious.

And there will always be questions. In some cases, U-boats torpedoed ammunition ships and were so badly damaged that they could barely manage to return to base; others torpedoed ships and were known to be damaged when a part of the ship collided with the U-boat as it sank. Some missing U-boats are known to have been in the vicinity of such occurrences and it's reasonable to surmise (although there may be no proof) that something like this could have sunk a U-boat without trace.

So, in truth, there's varying amounts of dependability of these accounts. But, to directly answer your question, I've seen an article by one researcher who says that at least 30 U-boats "just disappeared" with no reasonable explanation. Some sailed out of port and were never heard of again; others reported by radio that all was well and then disappeard. But it seems that in almost every case, the details and surrounding circumstances were slighlty different and different facts were known in relation to each one.

There is a paragraph on "U-boat Fate" for each U-boat listed on this website. (Go to the main page, click "All U-boats", then "All U-boats" again on the next page.) Reading some of those "Fates" will give you a good idea of the information that you're seeking.