in order to make latinum worth something, it is reasonable to assume that freedom of replication doesnt apply.
But "freedom of replication" should be seen as a relative thing. Dollar bills have value despite being made of worthless materials in a process that can be copied. Gold has value wholly disproportionate to the usefulness of the material itself. Future folks could easily continue to use paper bills or gold coins as currency even when replicators can create those essentially for free - the abstract value of those things would simply have to be coded into the items, like today's bills are transformed from toilet paper to currency by virtue of having a serial number.
The bottom line is this: no limitations have never been explicated for the replicator. Instead, it has been shown to be capable of astonishing things, with nary a shrug from our heroes when it does so. For it to be incapable of replicating substance X, something extraordinary would have to apply.
be something extraordinary, of course. But it might also be something as mundane as the silver out of which coins are minted.
The difference is though, that only the amount of latinum matters - standard coins (made out of various metals, such as copper-nickel alloy or copper-plated steel) and paper money hold a face value higher than their "scrap value" (i.e., the value of the metal in the coins, etc) because they constitute a promise to the bearer by the central bank of (insert-country here) to provide $X/£Y/€Z/etc worth of collateral on-demand.
GPL's monetary value, on the other hand, is purely a function of the quantity of latinum involved - as is made clear when Morn vomits up a small quantity of the stuff and Quark reacts as if he's been given the equivalent number of bricks. Thus, if it's not rare, the value collapses just as any market in a given substance collapses when the market's flooded. (and given the supposed energy surplus in ST times, if something can be replicated, it will be. Look at the tiny
quantity Morn vomits at the end of WMFM, which Quark claims is around "a hundred bricks worth!" - and the episode makes clear that 100br is a LOT - and even a fraction of a gram becomes more than worth replicating).