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Prefixing: I don’t think it is archaic in German, or a bad thing at all. It’s the German style of marking nouns when needed. However in English it is archaic, mostly unused since the 18th century.

As to your examples? Probably context, or the same way we in English distinguish:

• I saw her duck (she lowered her head)
• I saw her duck (she has an unusual pet)

All languages have ambiguity in some cases; it’s mostly fine. The examples you mention would be ambiguous when spoken [unless they also mark a pronunciation difference], so it is necessary to use that same context in that case.

Also note that a language that does have a way to distinguish nouns from verbs has a lot more leeway in using phrases that would otherwise be ambiguous, so they’re likely more common.