Not a scientist or science reporter, but it strikes me that the headline (and content) of the article should include 'that we know of'. Is that silly of me, or is it expected from the reader to know that this is always implied?
Yes, it's poorly phrased. It could easily say "oldest known insect plague". But the whole article is not written well at all - seems like English may not be the authors' first language.
No, there are different scenarios. In this case we're looking at incomplete evidence of history, and we know with certainty that there are many phenomena for which evidence didn't survive. The usual way this is dealt with is to talk about "the oldest known X."
With many things in science, there isn't anything like that degree of incomplete information. We can talk about, say, a chemical reaction with extremely high certainty.
Also, in many cases a theory provides implicit context which makes the resulting statements true in the context of that theory. We can say that in general relativity, a black hole has a singularity at its center. There's no doubt about that, but it doesn't tell us whether actual physical black holes contain singularities.
"Leaf miners identified as oldest insect plague in the history of Earth"