I have received a large number of integrity contraint violation errors relating to the catalogindex_aggregation_to_tag table; it turns out that it is one of three tables are related to the Layered Navigation cache:

catalogindex_aggregation

catalogindex_aggregation_tag

catalogindex_aggregation_to_tag

which quickly become huge even if tagging is not actively used.
The solution is to Disable Cache Control (beta) Layered Navigation” i the admin panel under “Cache Management” and then refresh the cache.
All three tables are then emptied and perforamnce is significantly improved.
There is a lesson to be learnt about using beta code, I guess…