I am going to start by saying that of course every family, every person is different and handles such days differently. I can only give feedback on how my family has handled the death of a young person very dear to us.
His mother and sisters--obviously those closest to him--chose, for the first several years, to be alone on the anniversary of his death. I am very close to my sister and she didn't even want to talk to me. For this reason, my instinct is that something that lets your friend know that you are thinking of her but puts no obligation on her to respond right away is best.
My instinct is that an email is best--just to let her know that you are thinking of her on this day, you are there for her, and as others have suggested, if you have a good memory to share about her son, that's lovely.
For some reason the flowers don't strike me as the right note--but then again, it is hard to see how anything prompted by the desire to comfort your friend on such a dark day could go too far wrong. It is kind of you to think of her--as others have mentioned, too often well-meaning friends are afraid to mention or acknowledge death, which causes its own grief.
As a further note, in our family we do not mark the anniversary of my nephew's death but his birthday, as we choose to remember his life rather than his death. You might be alert for any mention of your friend doing the same, or making any donations or charitable efforts in her son's name that you would feel comfortable supporting.
Again, it is very kind of you to think of her.