You are correct that a letter to the lawyer, even if notarized, may not rise to the level of a formal codicil, which is the appropriate way to amend a Last Will and Testament.
You may want to have an attorney review any documentation concerning the legal entity of your Uncle's shipping company: Operating Agreement, Shareholder's Agreement, or the like. You'll also want an attorney to review the letter and the Will. That will allow the attorney to have all the pieces of the puzzle before her prior to offering any advice.
A gift is not considered completed until the transfer is actually made and delivered. It may be that stock certificates would need to have been endoresed over to your Aunt. It may also be an issue that your Aunt was a witness rather than a disinterested non-beneficiary. However, if your Uncle's company was a sole proprietership, then perhaps an argument could be made that there was a gift. More information is needed.
It would be interesting to know who was to inherit the company other than your Aunt and if a buy-out could be arranged with those parties using other assets of the estate that your Aunt will, in fact, receive.
I suggest that your Aunt contact an attorney to review her options. Good luck to her!
The codicil must be signed and witnessed in the same manner as the will: by two witnesses, in the presence of each other.
I find it curious that the lawyer did not follow up upon receipt of the letter, or perhaps he did and the parties changed their mind about creating a codicil.