For the DS? The only encryption you are likely to encounter is the secure area stuff that some groups liked doing somewhat later on in the DS lifetime. If your tool complains then get eNDryptS Advanced http://www.no-intro.org/tools.htm on the case.
After that any one of a number of tools can be used to explode a DS game into its component files, and then reassemble it or inject them back in.
Popular tools include ndstool, ndsts (available on the link above), crystaltile2 and tinke.
Some games will pack everything into another archive or more archives but that is part of the fun of ROM hacking.
Not sure what goes for DSi stuff, though a scan around says there might be something out there.
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