The zen kernel shows up twice, is this just a visual thing that will be fixed with an update or is there something i have to do?
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It doesn’t appear to be an issue with the tool. At least in my mirror(and yours) the linux-zen kernel is in both the core and extra repos with the version in core being one point release newer.
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Is it advisable to keep using the zen kernel till they fix the repo mix up?
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It shouldn’t hurt anything. The newer version in core should have precedence over the older one in extra.
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I installed the core version, and it shows both installed, including the extra
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Ah you beat me to it! I was just about to post this, but good on you for catching it. I don’t normally open akm that often, but a post from just the other day got me to check it out and then I just opened it this morning after the recent update of all 3 kernels and saw it listed twice too in akm and thought hmm maybe this is something I should post about. But no need now, things seem to be okay in any case!
I’ll leave you with a screenshot showing the same thing to show you’re not alone 
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pacman doesn’t track the source of the package so I don’t think the tool would be able to tell you which one you actually have installed.
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Arch currently has zen in core and extra. I suspect that this is a temporary situation, and will be fixed soon.
The same can be seen with
pacman -Si linux-zen
And as @dalto said, core takes precedence. That’s because [core] is written before [extra] in file /etc/pacman.conf.
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