I've configured Exim to use syslog for its logs, with the main and reject logs sent to different files, but whenever a message is rejected, I get one message on the reject log and two messages on the main log.

You are probably putting your reject items into the main log as well; remember syslog levels are inclusive (for example, mail.info includes all higher levels, so a mail.notice message will be caught by a mail.info descriptor). Test this by running the command:

logger -p mail.notice test

and seeing which logs it goes into. From Exim release 4.31 it is possible to disable the rejectlog by setting write_rejectlog false.