Marr thinks the CE is an "electromagnetic collector", but that's probably more a description of how it eats than what it eats.
Nevertheless, the heavy implication here is that the CE eats people first and foremost, and the vegetation is but a side dish. Marr has studied its doings extensively, and draws attention to the fact that there were survivors this time. Generally, then, there would seem to be victims. And if those aren't surviving witnesses, then Marr probably doesn't suffer from observer bias where she'd only concentrate on planets where people were eaten: she'd find out about CE visits by some separate means.
Perhaps the CE indeed eats electromagnetism - mainly of the classic "life force" type so often featured in Trek and other scifi? Many a space beast has had an appetite for minds. The CE could be of a type that feasts on humanoid minds but stuffs its stomach with the minds of bacteria and grass when there's nothing better available - and needs to eat so much that going after vegetation-only planets isn't worth its while, when eating a planet with hundreds of people still leaves it hungry for a whole planetful of vegetation.
Total loss of vegetation might not be all that noticeable, though: Marr seems to think it might grow back in "years", although out of what, we don't learn. Perhaps the CE also eats planets where there are no humanoids, and the Federation just fails to notice because the planets recover in an eyeblink and thus don't appear all that exotic?
Timo Saloniemi