The up in the British clued up has a perfective meaning — as in give up, blow up, use up — which gives it the meaning of being well-versed on a topic, having a complete, or at least sufficient, knowledge of something.
The American clued in has the primary meaning, especially in the negative, of becoming aware of some fact or condition. Someone is in on something or completely out of the loop. The equivalent to clued up would be something like in the know or, to use an up-perfective instead of a spatial metaphor, up to speed.
So, for instance, the beginning of this article in the San Diego Union-Tribune:
Affordable housing developers aren't getting clued in on city land sales
17.02.2017 · Affordable housing developers are supposed to get first crack when San Diego sets out to sell city-owned land. For at least the past decade, they haven't.
For ten years, developer of affordable housing have apparently been unaware they have priority when it comes to city land sales.
Or from this marketing consulting firm:
Since they're [sales department] not aligned with marketing, they are not clued in as to what content already exists.
Or this post on a forum discussing an AARP discount on a car rental:
Instead of being a test of whether they could sell more cars to older customers the offer became a coupon good for anyone that knew about it or had a clued in sales dude.
The "sales dude" is aware of the discount.
On the other hand, American consumers expect the same level of expertise from a clued-in sales staff as Britons do from a clued-up one; they simply don't do it as often ("clued-up sales" 10x more hits than "clued-in sales").
Without a strong, clued-up sales team your business can't grow at its full potential. It is for this reason that sales training is so crucial...
Or simply pop into one of the above mentioned shops and have a chat to the clued up sales staff, who can introduce you to a world of options.
The hip and clued in sales clerks are a plus in this boutique with a decidedly New York energy.
If Coach [shoe store] is trying to position itself as a luxury store then it should hire more clued in in sales associates.
Sometimes, of course, the amount of knowlege sufficient to the task at hand is such that to become aware of something and to be fully versed are functional equivalents. So, for instance, in two restaurant reviews:
Great service and staff very clued in about gluten free choices, which was great.
Staff are completely clued up about gluten free, never had the slightest problem with it as everything is separate.
In the same way, one can be clued in or clued up on the meaning of particular words:
Make sure you get clued up on the meaning of a number of terms, ranging from each-way betting to forecasts and accumulators, before handing over your hard-earned cash to the bookmakers.
Us Twin Citians don't need to be clued in on the meaning of La Cucaracha.
To judge by comparative Google queries, Americans can be clued in on problems or difficulties, while Britons are not clued up about them, yet Britons are invited to be clued up on any number of topics from autism to wound care. Americans, however, are rarely clued into whole fields of knowledge or broad topics without further qualification. If the two expressions were indeed identical, then one would expect a similarity in usage more easily established in actual, unfiltered language.