In the current implementation, ships drain some amount of supplies per day as long as they are active, regardless of the number of crew they carry. This indicates either a fuel consumption which is separate from the fuel used for hyperspace, or regular maintenance and replacement of worn-out parts, or both. I see no reason why the ships would drain food, and I see no reason why changing things from 'supplies' to 'food' and 'repair parts' would remove the supply drain due to ship maintenance. Therefore, if ships retain their current characteristics, then splitting 'supplies' into 'food' and 'repair parts' will change things from having one constantly draining resource into two constantly draining resources. I fail to see how this is better than the current model, nor do I see why the current maintenance cost of ships would go away just because we now have 'repair supplies' and 'food' instead of 'supplies'.
Also, routine maintenance will always involve non-edible supplies of one kind or another as nothing will ever be designed that can last forever. Proper lubrication and replacement of old or worn-out parts are both part of routine maintenance, and neither one of those generally consumes things which fit into the 'food' side of supplies; both, however, consume things which fit reasonably well in a 'repair supplies' category. Routine maintenance also does not typically require significantly greater food consumption than normal; it certainly isn't enough to justify a food cost for a frigate equivalent to the supply consumption of 200 crew.
One further note - there is no 'CR/Logistics/Repairs triple whammy' - the logistics cost of a fleet is equal to the sum of the number of supplies per day that any given ship can spend recovering CR, plus 1% of the total crew carried plus 2% of the total marines carried plus 10% of any crew/cargo/fuel surplus plus any current repair supply usage. CR recovery has no effect on the logistics rating, because the logistics rating already assumes that the ships are consuming supplies at the full rate required for CR recovery even when the current supply usage is only at the maintenance level rather than the recovery level; if it were otherwise, your little frigate at the start of the game would suddenly cost 10 times more logistics after every fight regardless of whether or not you picked anything at all up after the battle. A fleet's logistics cost is equal to its supply usage with the assumption that the ships are recovering CR; there is no feedback into supply usage due to the logistics rating except in the rare case that your logistics rating is pulled below its normal level for a sufficiently long period of time for the CR of fleet vessels which had full CR (or, at any rate, a higher CR than the limit imposed by the current logistics rating) to suffer significantly.