Right upfront, I’ll say that I don’t know. All I can offer you is my reasoning, but there’s nothing that Funcom actually said about that specific building technique. So if anyone is looking for some definitive verdict, feel free to skip this post.
Before we talk about ceiling stacking, let’s talk about fence foundation stacking again. If you take a look at the rules, they don’t mention fence foundation stacking at all, just like they don’t mention foundation spam. The rules are generic, not specific.
So why is fence foundation stacking, specifically, a problem? And why are people who use fence foundation stacking getting banned? To try to answer that question, we have to look at how and why people use fence foundation stacking.
This is one of these cases where a picture is worth a thousand words, so let’s take a look at one:
The picture above is from a thread that’s more than 2 years old now, and I imagine that the technique is much older than that. But it’s an excellent illustration of what people are talking about when they say “fence foundation stacking”. They’re not talking about the ability to put two fence foundations close to each other, they’re talking about a specific application of that ability.
In other words, “fence foundation stacking” is not just a building technique, it’s a specific application of that technique, used as a defensive strategy on PVP servers.
Since I don’t play on PVP servers, I can only speculate about the players’ motives for building like this, but unless I’m missing something, it should be pretty obvious: since there’s a 5-hour window each freaking day during which you can get raided, regardless of whether you’re online to defend your build or not, people who want to play on PVP servers but can’t spend 5 hours every freaking day have to come up with some way to make offline raids less effective. Building densely layered fortifications like this is one of those ways.
Naturally, everyone and their grandmother got used to building like that on PVP servers. Hell, for a while, it was even “officially okay”, if you knew where to look for a confirmation.
So why are people getting banned now? Because one of the rules prohibits building in a way that leads to “loss of performance both on client and server-side”. Look at the picture above. Now try to imagine what it’s like when the server has to send all of those building pieces to several game clients at once. “Normal” builds are not as dense as that monstrosity above, so when parts of a base come into the render distance, the server has to send less data to the client.
Anyway, why am I going on about this? Because it’s important to understand that Funcom isn’t (supposed to be) banning people merely for placing fence foundations close to each other, but rather for doing it in a way that is likely to screw up the performance.
So can you use ceiling stacking in your builds? If you want to convince yourself that you have no chance of being banned for building, then the answer is “no”. Because let’s face it: Funcom could ban you, if they wanted to, without any reason, and there’s nothing you can really do about that, so there’s no way to be invulnerable to bans, only a way to convince yourself you are. 
Would I use ceiling stacking in my own builds, in a limited way, for example to “laminate” some foundations that I want to look different, or to build a shallow staircase, or something equally restrained? Yep. Can I get banned for that? No idea, I’ll let you know if I use it and get banned. 
To anyone who wants assurances: sorry, “common sense” is the best I can do. 