In fallout 3 does the nuka-cola machine restock in tenpenny tower

If you are talking aobut the machine in the player home; then no. You must put Nuka Cola in the machine and it will turn it into Ice Cold Nuka Cola. This does not work with Nuka Cola Quantum; and the Ice Cold Nuka Cola cannot be used in place of Nuka Cola in Crafting Recipies or the Quantum Chemist perk (which gives you 1 Nuka Cola Quantum for every 10 regular Nuka Colas in your inventory).

If you mean a different machine; then yes, I think they do regen after a while.