Only very special cases, such as the 8,000-people Tarsus colony in the "Conscience of the King" backstory, depend on external supply.
Tarsus Four had it's own food attacked by an exotic fungus, the majority of the food was destroyed. That's why they needed ships to bring in food.
For actual creation of matter, replicators use plasma that powers the ship and convert it into matter
The plasma in the warp core is already matter, it doesn't have to be converted into it.
The warp core is filled with hot ionized hydrogen gas (deuterium plasma). It would take about 18,000 cubic meter of hydrogen gas will give you 1 liter of water.
You should drink at least 2 liters of fluids a day, more is better. The crew of the Enterprise Dee would consume over 2 metric tonnes of drinking fluids per day. That's 36,684,000 cubic meters of warp plasma being used daily just to produce water.
We know the very same process occurs in Supernova's in real life (conversion of energy into matter).
If you are referring to nucleosynthesis, you have it all wrong. Nucleosynthesis in no way converts energy into mater, but instead it is a process by which heavier chemical elements are created using hydrogen and other previously synthesized elements. Energy is used in the process, but is not converted into matter.
The Federation (if anything) is basing their technology on how nature works
And what you're describing doesn't work. Neither through "creating" matter out of energy, or by siphoning off plasma from the warp core to use in the replicator.
The technical advisers on the show produced a technical manual (nope, not canon), the replicator is described as employing base stock materials, which are altered by the replicator into the desired product. These base materials have to be periodical restocked owing to a recycle efficiency of 82%.
... but that basically comes down to writers being uninformed and dumbing things down.
Really? Sound like they had it right.
They do have recycling capability which effectively converts matter into energy
Okay, what kind of energy then? By what you've posted, obviously not energy in a physical form. So it isn't just sitting in the EPS, because electro-plasma is a form of matter. What kind of "energy" did you have in mind?