OK, I should be careful here because I am in the limbo between law school and having a license, so I cannot provide legal advice. But, I will say that it's important to remember the different types of protectable intellectual property.
When we say a company's trademark work, it's a bit confusing. Trademark usually refers to the name, logo, etc. but can also can refer to headstock shape, inlay type, etc. (see Fender, Gibson and PRS). What makes the trademark issue interesting is that it is not the functionality of the feature that is protected but the non-functional aesthetic aspects. So, trademark doesn't really help when it comes to functional designs like circuits and pickup design. What trademark is designed to protect is against the likelihood of confusion as to the source of the product. If the circuit board says BoogieMan in big letters and does not say Alembic, then there isn't much likelihood of someone thinking that it was made in Santa Rosa. It might argued that the shape and configuration of the two pickups and humcanceller in the middle could be a trademark configuration. When I see that, I certainly think Alembic.
But patent might useful. If the design is sufficiently unique and non-obvious (among other attributes), then it can get a patent. I don't know for sure if Alembic got a patent on its system (humcanceller, filters, etc.) but even if they did, it would have expired already unless they had managed to renew it. Given the huge cost of getting a patent, it might not even be worth it in this case, since it's not a design that is or would probably be in common use. Defending the patent would be pricey as well and licensing it would not bring in all that much revenue.
Copyright is also something that can be brought to bear and could apply to circuit board design. However, it would apply to the exact layout and design and it's not always clear if it is something the courts would uphold. Mike is right, if Boogieman changed the layout enough, even if the design is functionally the same, it is not protected. Where people have gotten into trouble is when the whole board is directly copied, sometimes even including the original in-house company designations and/or name and logo! Opening a device from Company B and finding a circuit board labeled Company M is a serious problem. I don't think that is the case here.
Trade secret can be used to protect intellectual property, but it is subject to reverse engineering, which in this case would be pretty simple. So, there isn't much help here.
At the end of the day, what really protects Alembic from Fernandes and BoogieMan and other imitators is not the legal world but the fact that real Alembic instruments are real Alembic instruments. We know the kind of care and craftsmanship that goes into each one and we know that it is extremely costly and difficult to match that. The reputations of Ron, Susan, Mica, et. al., including past contributors to Alembic who have gone on to their own stellar careers, make it clear that the real value is in the original instruments. When it comes to things like circuitboards, I don't see it as too consequential because to be really useful, you need an Alembic bass, which means that you already have the circuit board and the pickups and have little need of purchasing the copy. Alembic is largely protected because they are Alembic and anyone who gets something that is not Alembic knows that they are not getting the real deal. My sense is that Boogieman or other copiers of this type are not really going to make much out of this or put much of a dent in Alembic sales. I would imagine most of them just quietly disappear after a while.
Again, I'm not really a lawyer, I've only played one at final exams at school, so please do not base any action on any of these statements. Despite my analysis, there might be a very real argument to be made in court on behalf of Alembic. To quote Frank, I might be totally wrong. Hopefully one of our real lawyers can chime in.
