Hmm, some stray thoughts-
Spice of course was the ultimate commodity for Dune, being critical to navigation, life extension, more or less hyperanalysis by those able to use it, and cheap enough on Arrakis itself to be a feedstock for local production.
We could extend that to say various commodities back such and such currencies.
Another scifi example that comes to mind is Norstrilia, where Stroon is the ultimate commodity, and there is obviously a complex currency system based on jumps, SAD and FOE money. You can read it here, a bit from the novel-
http://indbooks.in/mirror1/?p=260758
But for the OTU, we have to consider the milieu, specifically that it's a gameplay construct and secondarily that construct needs to be internally consistent to make sense and generate scenarios for play.
So, in thinking about the CrImp and the Imperium, we have to consider that it's primarily a huge trade union that is focused largely on that function, does not get into world issues except to the extent some moron somewhere threatens that world's 'total value', trade or otherwise, and invites massive response.
As such the Imperium is going to want to make trade as easy as possible, with among other things a stable currency and settled up accounts.
So there is going to need to be a physical currency for every day dealings and as noted operating costs of ships and underhanded trade and all that.
Rare metals, heavily encrypted scrip, subatomic bonded atoms that spell out a registration number, all that.
But there is also going to be a huge pile of interstellar transactions that need to be done securely and with minimal lag.
If it is possible to write 'bad checks' or withdraw funds against insufficient funds across multiple worlds ahead of the wave front of reconciliation communication, no government or bank is going to be willing to deal with that and trade collapses, or moves with the overhead and cost of physical currency, or worse lags by x-boat and subsidized mail. Not acceptable for the Imperium's very reason for being.
So let me suggest an addendum.
Within a system, the transactions are done on deposited physical money and locally transmitted electronic credits.
It is possible for a ship to go months and just pay and be paid off of credits that are local to that planet plus ship's credits. Major corporations will typically have enough deposited locally to handle system business plus small emergency contingencies.
For interstellar transactions, drawing or paying on an account in another system, the transaction must be centrally verified to finalize.
This function occurs at clearinghouses located at the subsector capital. Conveniently the capital is typically on a primary x-boat route, and will have subsector financial/trade courts for dispute resolution.
So this will typically be between 1-4 weeks going to, then coming back with the confirmation/transfer.
This would be bank transfers, heavily encrypted transactions by TL15 computers onto 4-D matrices that are constantly changing. Another word for it is 'mail'.
A ship's mortgage payment would typically be deposited in a local system, the transaction then shipped off to the subsector capital clearinghouse where it would be permanently credited.
Subsector capitals therefore are aware of most currency matters at least as they pertain to banks and large scale dealings.
Subsector-to-subsector transactions then go by mail from one subsector capital clearinghouse to the next. Such a transfer requires physical presence and authorization at the originating subsector capital.
Physical currency minting should be a ref choice, whether centralized and shipped in on treasury ships, or locally minted likely at the subsector capital.
This way, the Imperium can manage it's currency state, and you as the referee can figure out the timing of any shenanigans by PCs or NPCs alike.
An optional thought- rather then wait on payment going through, the recipient of funds could choose to bond their transaction and cash out. The bank takes out 5-10% of the payment and bonds it, half as payment to bonding companies and half as profit for taking the risk.
Of course, the payment could fail to go through without PC fault due to NPC negligent or criminal behavior. The bonding companies could have really good lawyers and/or are more of a 'streetwise' thuggish collection nature, which could spell trouble for Our Heroes if they can't clear their name.