There was a time when we had all our priorities screwed up. I remember encountering a cook many years ago on an OSQAB course (now we call it NETP?) who had been serving in ships for four years. Now that he was finally loaded on the course, he had a posting message for Petawawa and was leaving the next month! It's nothing close to that anymore, but we still have occasional problems with personnel posted to ships without first having done the appropriate ship training.
Generally, they want you to be posted to a ship before they load you on the course, simply because the training has an expiry date. it's only good for two years. If you do the course too soon, you will simply have to do it again when you are actually posted to a ship (although it's a refresher course the second time around and so somewhat abbreviated). As Comm Rsch, there are a very limited number of shipboard positions, so it could be a long time before you actually get to sea. Nevertheless, it never hurts to ask. If there is nothing more constructive for you to do, they might let you do it if there are spaces available.
On a final note, sea duty allowance (SDA - "sea pay") is not dependent on having done the training. If you're posted to a ship and have done your in-routine, you get SDA, period.