I was so shocked to hear this, I reached into the Punctuation Pocket of my Word Hoard to reassure the waiting semicolons. No only do I not hate them, I brought cookies to show how much I love them.
I left Otto, the Czech speller, to clean up the resultant mess: sn;ick;er;;;doo;;;dles;;;;;mall;;oma;;rrs;;;;;;choco;;;olate;;;chips;;;;
The idea that anyone who wrangles words would hate any one member of the punctuation platoon is perplexing to me.
Punctuation is like the nitrous oxide used in The Fast and the Furious; you start with a fast car and an expert driver but it's the NOS that provides the extra kick you need to hit the finish line ahead of everyone else. Which is exactly how you think about querying, I know.
Deft use of punctuation can give your work power and punch and panache.
To rob yourself of any piece of punctuation is idiotic.
If an agent says s/he hates semi-colons, my guess is s/he's seen them abused too often, but that's like blaming the victim for the crime.
I don't hate ellipses even though some writers fling them about with abandon; as if they'd bought a barrel, suspended it over their computer and dripped them down on the manuscript like faux freckles.
Generally I frown on that ... but not always.
My favorite piece of punctuation is the interrobang.
And there are some lovely new ones to add to our repertoire
But the bottom line is this: beware of blanket statements from anyone, but particularly from agents, about what the agent horde does/does not like. Lacking any kind of context, or punctuation indicating irony or sarcasm, you might well misinterpret.
Plus, there are only a few industry standards.
There are a LOT of preferences.
Mine, of course, should be industry standard.