Hmmm, that's a tough question. XSLT doesn't provide a way to supress xsl:output, you can only override them.
I see a couple solutions:
1. Transform imported stylesheet to filter out doctype-public/doctype-system attributes of xsl:output before applying it. XSLT is just XML so it's easy. A drawback is a temporary file.
2. Trick - when using -mo option xsl:output instructions are currently just ignored (along with disable-output-escaping). It's pretty safe from XSLT processing point of view, but I can't guarantee I won't change it in future nxslt versions. .NET 2.0 actually allows me to fix this deficiency.
Well, unfortunately nothing in XSLT spec says that doctype-system="" means no Doctype, so most XSLT processors just produce <!DOCTYPE foo PUBLIC "" ""> in this case. And .NET 2.0 too.
For nxslt v1.X I can extend my filtering reader (that takes care of extension-element-prefixes) to filter out doctype-system/doctype-public attributes if some command line option is specified. That sounds easy. But for nxslt2 must be a better solution.