Once you have the DB server separate from the webserver -- load balanced clusters, for example -- it may help, though marginally. Bonded NICs will give you more throughput (bandwidth) between webserver and DB server, where what you _really_ need is better (lower) latency.
To get better latency what I'd perhaps do is link the DB server to the webserver over a dedicated direct connection. I mean - no switch, crossover cable. Simple is fastest
By the same token, if bonded NICs mean higher latency (and they very likely will) they will hurt performance. I'd tune/time/benchmark the hell out of it until I'm sure the latency is as low as possible.