I released an update to SimplenoteSync yesterday that fixes an issue where the script would download a note just to “verify” it was flagged as deleted, when it should know this from downloading the index.
Basically, this fix should make the script run faster and hit the server less often.
It also adds a flag to log network activity - if it seems to be running slow for you, enabling this flag will let you know each time it hits the Simplenote web server. They were seeing some increased activity, most of which was probably from improper user configuration (e.g. running the script too often), but this will certainly help some.
Please update, and as always — BACKUP YOUR DATA!