Strange. From your post, all the "usual" reasons this might happen are ruled out.
A few guesses. For one thing, stay out of Truth when assigning weapons. It won't work when Truth is on. Another stab in the dark is that you might be on the wrong sub-page. Fire control is divided into 3 sub-stations, and when you say you've clicked on the number I suppose it's possible that you might have meant the number from the Launch Panel instead of the target display. Make sure you're at the target display.
Another guess is that you might be clicking the wrong number. The Akula has external and internal tubes, so if wanted the 53cm in internal tube 1 but external tube 1 had a LAM and you accidentally clicked external 1, then it won't assign.
Not all torpedoes can be assigned to attack submarines. Make sure you're not assigning a wakehomer.
Wire guidance is accessed from the "W" beneath the tube number, or by clicking the weapon itself on the fire control map. Not all weapons can be wireguided (53cm and 65cm for stock DW).
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