I've done this a few times and it's always been counted as single baggage. In fact, this year Scandanavian airlines has actually advised me to do this.
I did this with Ryanair last year. Put the panniers in one of these Ikea bags with a bungee around it, I think they do a zipped version as well for about £1..then bin it at the other end. If no Ikea nearby they are on Amazon or ebay. No issues.
To avoid the bags catching / snarling on the conveyer belts avoid the bungee straps, gaffer tape is best. Flying back from my last tour I just used dustbin bags with gaffer tape, and even with a connecting flight, i.e luggage transfer the bags were fine.
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