I was a navy nuke and I did a recruiting tour prior to getting out in 03. I can answer a few of your questions based on what I remember.
First of all, I did have success with age waivers for the nuke program, but I don't remember ever having to do an age waiver and a moral waiver for the same applicant. Marijuana possession was a big deal for entry into the nuke field and is never taken lightly. If that is all you have on your record, I can see them possibly approving it. As far as both waivers getting approved, unfortunately I don't know what will happen. At some point you will probably talk to the XO of the recruiting district and you need to be able to explain to him why you went wrong and show remorse. He will be the one that forwards his recommendation for the nuke field waiver.
As far as the AECF program is concerned, it is a good program. Generally, the nuke field would be thought of as the top enlisted program to enter and AECF would be 2nd. If you are willing to enter the AECF program, I would go to MEPS and join under that program (with the hopes of getting the waiver). If you are not willing to enter the AECF program, do not go to MEPS and join.
Being a former recruiter, I know your objection to joining as AECF and waiting for the waiver for the NF would be, "Will they change my program to NF or are they just telling me that?" I can tell you this, if your waiver is approved, they WILL switch your program. The Navy always needs nukes and the recruiting districts are given NF goals that they need to meet.
If you are set on joining the NF and not AECF, I recommend trying to get your waiver pushed through prior to going to MEPS. I don't know if they will without your physical complete, but it's worth checking. If they won't, you need to ask your recruiter to let you go to MEPS for a physical only and then wait for the waiver. You need to make that very clear, because they WILL try to get you to join when you go to MEPS. I can't emphasize that enough. This is much bigger than your recruiter. Recruiting districts need to make goal and every effort will be made to get a qualified applicant on deck to join.
Best of luck!