Another interesting thing that happens is you don't necessarily know what form your actual optimizations will need to take. Later when your systems grow you discover the suboptimal parts you hadn't optimized for.
Very early on at Cloudflare I worked on part of the DNS infrastructure that took DNS records from the UI and got them in a state for actual authoritative serving. The system had been constructed anticipating Cloudflare having millions of customers with unique domains, but it had not been constructed for a single customer with a single domain with millions of records. This caused a periodic slow down in DNS record updating while the system churned on that one customer.
In a different job I worked on a piece of optimization software that needed to keep track of "node" A is reachable from node "B". This had been implemented as a matrix (literally a malloced NxN matrix of ints storing 0 or 1) which worked really well for small systems. But you'd be out of memory really fast on a large project. I replaced the matrix with a hash table and all was good because the matrix was actually really sparse.