Any mods applied? Some of the mods, you have to "load" the torpedoes. Try pressing the "Load" button and see what happens. Once you fill the stores initially, sometimes you have to "Re-fit" again in order to fill the reserves... btw, is your crew possibly still at "battle stations", maybe even "silent running"? If you have v1.5, those show in the upper right of the screen. I can't remember if v1.4 does...
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