In embedded world, memory often needs to be exactly controlled, and allocation failures are fatal without a more complex MMU. In kernel world, I believe the main reason is that allocations can block.
In addition, a lot of data structures might be shared across multiple cores. Linked lists can be traversed and mutated concurrently (although with a bit of care).
I'd be convinced once I see pure Rust kernels geared towards modern machines suddenly using linked lists everywhere. Otherwise I'm leaning towards it being a side-effect of the language choice and culture.
Also because I've seen the same kind of reasoning applied to compilers (e.g. "of course you need linked lists in compilers, they are extremely graph traversal heavy"). But one look at modern compilers implemented in Rust paint a very different picture, with index-based vectors, data-oriented design and flattened ASTs everywhere.
It can be solved (or worked around), but it's understandable that people don't _want_ to do that.
I/e in a DMA-based ethernet driver, the ethernet MAC receives packets asynchronously from the processor, perhaps faster than the processor can ingest them. So the mac interrupts the processor to give it new packets, and the processor can't sit processing the packets in the interrupt context, so it needs to put them into some ordered list for processing later when it has downtime. In a true embedded system, the memory for this list is going to be fixed or statically allocated, but you still don't really want to have an array-style list with fixed indexing, as you'll have to manage what happens when the index wraps around back to 0 etc, so instead you just construct a linked list in that pre-allocated memory.
I wouldn't say linked lists aren't really used in high-level applications, as I said they're used all over the place whenever you have external asynchronous communication, it's just that modern high-level frameworks/libs totally abstract this away from most people writing high level code.
My experience in embedded, everything is hardcoded as a compile time constant, including fixed size arrays (or vectors of a fixed capacity)
A common way to implement these is to have an array of messages, sized for the worst case scenario and use this as the message pool.
You keep the unused messages in a single linked "free-list", and keep the used messages in a double linked queue or fifo structure.
That way you get O(1) allocation, de-allocation, enqueue and dequeue operations for your message queue.
Another example for this paradigm are job queues. You might have several actuators or sensors connected to a single interface and want to talk to them. The high level "business" logic enqueues such jobs and an interrupt driven logic works on these jobs in the background, aka interrupts.
And because you only move some pointers around for each of these operations it is perfectly fine to do so in interrupt handlers.
What you really want to avoid is to move kilobytes of data around. That quickly leads to missing other interrupts in time.