Link for context of discussion
(My opinion, just to clarify)
Use of computer-printed material should be cleared through plot on a case-by-case basis. Generally speaking, anything that is not "organic" should be cleared through plot. For instance, actually setting up a tent in the woods somewhere remote, but within the bounds of being "on-site", shouldn't need to go through plot, while claiming to having a tent hidden off in the trees, in fact, should.
The primary difference is whether or not a player can reasonably use the "Live" physreps to try and trace something down without the intervention of plot, whether its a piece of writing, a tent in the woods, or a hidden compartment in a cabin.
If it is possible, within the bounds and context of the game environment, to trace it down, then it should be allowed. If, on the other hand, it relies on resources that are not traceable on-site without the intervention of plot (ie, scribes, printing presses, privateering ships, etc.), then it should be cleared through plot so that they can appropriately address questions that will inevitably come from the PCs.
Having covered the basic philosophy, here are my direct answers.
Should PCs handwrite everything they use in game?
If they do not want to clear it through plot, yes.
Should using printed letters equate to using a scribe?
Printed letters (computer-generated, typewritten, etc.) should equate to having been generated by a plot-resource, whether that is a scribe, a printing press, etc.
Should you have to pay that scribe?
For generic activity that you expect no particular secrecy with, no (i.e. public contracts).
Should plot be able to use that scribe as a way to gather information?
Yes.
Should you be able to pay more for a more discreet scribe?
It depends on how you obtain the retainer. For instance, people who use the Economy packet pay a flat fee at the outset. For that fee, it is presumed that by and large, the crew, house servants, or caravan flunkies are loyal to you. However, there are specific mechanics that allow for being betrayed (the mutiny bead, in Ships, for example), and, as always, Plot holds sway over your Ships.
Similarly, using pre-printed material and the secrecy thereof depends entirely on the source. If you are a "pay-per-use" kind of contractor (and expend no game coin), then you get a guy who prints stuff out for you. If you want to pay for secrecy, it should cost actual game coin (rather than virtual between event coin), and ultimately, is governed by your IG relationship with the NPC. OTOH, if you spend some chunk of money for a printing press and staff, or otherwise obtain a tag for such, then you become more visible in having the means (IE, you get an asset tag from Plot), but generally speaking, the staff that administers it should be loyal to you (whether that is a typesetter, or the guy you buy your ink from), for the most part (again, with Plot having final say on events that can or might occur).