First let me say that I have never used panniers. Nor did I even consider it when I was looking at buying a trailer.
I bought a B.O.B. Yak trailer last year. I plan on doing some week end self contained touring trips this year. And hopefully make longer trips next year.
So far I have not towed my trailer with anything in it, only towed it empty just to see how well it would track behind my recumbent. It tracked beautifully, never lost control, hardly knew it was there, when it was not bounccing because of the bumps.
The only disadvantage I discovered was it bounced like hell when ever I hit a bump. But I knew that would happen. But I never lost control because of it. Other wise I hardly knew it was there. The next time I tow it I'll put some weight in it so it does not bounce..
Yes I could tell there was a weight differance. But I knew that would happen too. It only slowed me down by about 1 mph, if that. I'm sure that when I put weight in it I'll be a little slower yet. In fact I expect it.
It is probably a safe bet to say that the slower speed due to the weight of both towing a trailer and using panniers is about the same.
One great advantage that a trailer will have over panniers is once you get to your destination for the night and after you set up camp you can leave your trailer at your camp site if you need to go into a town for something to eat, etc. With panniers you will at least have the racks still attached to your bike and maybe one of the bags. Meaning you will be hauling more weight even after you get to your over night stop. With a trailer that is not a problem. You just un-hitch it and off you go.
A long time member of my bike club who has done several self contained trips to Colorado and back and points further west told me one of the more ideal ways to tour these days is with a recumbent and a trailer. He has always used wedgie touring bikes with panniers.
I asked him why he did not switch when he bought his new comotion touring bike. His answer was he is so used to touring the way he has he didn't want to make the switch. Which was to me a very legitimate answer. But he did suggest that anyone new to touring do so at least with a trailer, but he also recommended a recumbent too.
Funny thing is he has never ridden a recumbent but I understand what he meant by his answer.
At the time I talked with him about this I had not purchased my trailer yet, but was looking into it. He also told me that when he started his self contained touring he wishes that there were trailers available for him to use.