Where is the incentive to update the Merkle root I've just read the following question 
Does block size effect Miner&#39;s Hashing speed?

and it appears that the answer is no - since miners only need to hash the Merkle root.  

However, updating the Merkle root will take a lot of CPU power if/when bitcoin transactions reach a rate of 4000 tps.

What is the incentive for miners/pools to expend effort maintaining the merkle root at this rate?  Obviously if they do not expend this effort the result will be an ever growing backlog of unverified transactions.
The merkle root ensures that transactions were part of the block that is being found. It links the block header to the set of transactions in the block.

So if you don't update the merkle root you are not actually confirming the transactions, and you won't be able to collect the fee of the transactions. So the incentive to update the merkle root is the same as for including transactions into a block: you get transaction fees for doing so.