Does the 5th amendment right to avoid self-incrimination apply only to the particular charges being brough in a given case, or does it cover any statement that could be incriminating, even if it were in a different proceeding, or if the record from Case A were to be used as evidence in Case B?
No, it applies to all cases ... if you state something in case A, it can be used in case B. Which is the point of the protection: if you are on trial for jaywalking, and can "prove" that you were not jaywalking because instead you were robbing a bank across town, the law cannot compel you to state where you were (thereby confessing to some other crime). You can volunteer it / waive your right (and be an idiot), but the law cannot force you to confess.
If somebody were being charged for one crime that probably left evidence on the HDD(kiddie porn, say); would the fact that they know that there is evidence of CC-skimming(but, unlike the kiddie porn, the feds have no circumstantial evidence or other grounds for belief) justify a 5th-amendment refusal to decrypt the volume? Would the other potentially-incriminating stuff be irrelevant because it isn't among the charges(even if the court record could be used as evidence to bring future charges)? Would the suspect be compelled to divulge the key; but the prosecution only have access to material relevant to the charges being filed, with some 3rd party forensics person 'firewalling' to exclude all irrelevant material?
I didn't see the warrant specifically mentioned, but "normally" the search warrant has to specify exactly what is being searched, and is thus ONLY valid for what is being searched. For example, the search warrant would say "the file named kiddie_porn.jpeg", and thus only that file (and not ccfraud.txt) becomes evidence. That said, warrants can also be broad - the hard drives themselves were presumably seized because the search warrant said "any computers and electronic storage devices located at 123 Perpetrator Street". Fishing expedition warrants saying "all files showing evidence of kiddie porn" tend to get thrown out, but a warrant saying "all files under C:\kiddie_porn" backed up by evidence (a P2P log) showing that files in fact were placed within C:\kiddie_porn is probably valid - and a warrant backed up by a P2P log is almost certainly what the search warrant this judge is ruling about says.
Not being a lawyer, I can't tell you what happens if the person examining the encrypted contents happens to see evidence of some other crime. But the physical analogy is this: if the police show up with a warrant to search your house for "computers", they are obviously entitled to seize all computers. And if they walk through your house and see illegal drugs sitting on the table, that's admissible evidence ("in plain sight") (Interestingly, it cannot be seized because the warrant does not specify "drugs". But what happens is the cop calls the judge and says "I'm executing warrant A for computers and see drugs on the table, can I get warrant B to seize the drugs?" and the judge faxes over a warrant right away). But they are not allowed to rifle through all your drawers and closets - drugs found there are not admissible evidence because they are not "in plain sight". (Unless you give the police permission - and they WILL ask. Which is why lawyers always advise saying "I do not consent" - you cannot stop the search / seizure, but not consenting makes any evidence found without a warrant inadmissible and the police potentially liable for misconduct). It's difficult to guess how courts would apply this standard to searching a HDD, but they would do it by starting with the physical analogy and figuring out how it applies to electronics.
What's happening in this case is that the prosecution knows files with kiddie porn names were downloaded. But they still cannot prove the files contain actual kiddie porn. (Maybe this guy is sick and thinks naming his legal porn files with kiddie porn names is funny). So the prosecutor was hoping to compel this guy to hand over the encrypted files (whose names they knew), under a warrant that compels him to be truthful about their contents (by having a neutral 3rd party do the work). The judge decided that the prosecutor does not have enough evidence to prove this guy actually knew what was in the files (maybe he operates a repository with files stored on an encrypted disk, but does not himself have access to the files). The judge also implied that if the prosecutors DID have evidence of what was in the files (maybe 1 or 2 got left on unencrypted drives by the P2P program as intermediate files and the filenames matched?), he probably would authorize the warrant and require this guy to decrypt his drives.