Very valid point. I don't think it's a problem having lots of items with no use in progressing the game, as long as you don't have it so an item starts off as an ambient item and later becomes a usable item. Gray Matter did this a few times and it really bugged me as it meant that every chapter you had to click on things you'd already clicked on just to see if they were now usable.
You could do something as simple as have the avatar say something to himself after getting information that seems of more importance like "hmm, i think i'll take a note of that" or "that could prove useful later.." and have a log where he keeps track of his progress including codes and such he gets from computers. The audio cue will register in the player's subconscious making that info feel more relevant than the bits without an audio cue, and the log file will prevent backtracking when you forget a code or something.
As for puzzles with multiple solutions, i'm all for that but i think you have to be careful not to make one solution easier than the other, or you'll have some people feel cheated by the experience. So if you have one puzzle where the player has to make a magnet, then you should have a similarly difficult puzzle involved in the player finding the key to open the locker containing the ready made magnet.
And as for a cluttered inventory. The setting of your game makes for some good possibilities to unclutter the inventory at regular intervals as part of the story. Perhaps your character gets caught in an area of the ship with a hull breach and some items get sucked out of his pockets, or perhaps there's an area of the ship with a metal detector and won't let him pass with certain items, or a bio filter which won't let him pass without dropping some items of an organic nature. Of course they would have to be choke points otherwise it'd be possible for the player to lose items they might need later on.
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