Why do Nodes accept blocks that have so many intentionally excluded transactions?
Because nodes do not get do discriminate between blocks. If a block follows the consensus rules, it must be accepted. If it doesn't it must be rejected. If nodes instead each have their own rules, they risk getting forked off from the rest of the network, and the currency.
Now one can of course wonder: why don't the consensus rules say something about rejecting blocks that have too many expected but missing transactions? The simple answer is that that is not a consistently enforceable rule. Nodes' mempools (the set of unconfirmed transactions) are not, and cannot be, guaranteed to be consistent. There can be double-spends on the network for example, which cause some nodes to see one version first, and other nodes to see another first. When a block finally arrives, at least one of both sets will be wrong. Some transactions can also be slow to validate and to relay across the network, so when a block arrives with it in it, some nodes may simply not yet have heard about the transaction.
Simply put: an expectation of what is in the next block is only useable in consensus rules if we can guarantee that all nodes, at all times, agree on what that expectation is. And to achieve that, we'd need an algorithm for consistency across unconfirmed transactions. If we had that, we wouldn't need a blockchain anyway, as the blockchain's goal is a consensus algorithm, exactly with the purpose of getting everyone to agree on some piece of data (confirmed transactions, and their order).
Isn't that against the Bitcoin ethos in a sense since this is akin to censorship?
Quite possibly. But all it needs is some miner, possibly anonymous, to start mining these left behind transactions. The whole point of mining, as opposed to a central coordinator that decides which transactions are accepted in the presence of conflicts, is that anyone can participate.
Do some nodes purposely attempt to not accept these miners blockchain?
That too, would increase the risks of irreconciable forks. Unless a majority of the hashrate enforces such a rule, choosing not to build on top of some censored set of miners' blocks, is just creating a minority fork that will be ignores by the entire network. With a majority of the hashrate enforcing it, it is possible. But then we call is a 51% attack, because unless it happens with agreement of the whole network, that actually is censorship.