If I were taking a 87-year old mom across the globe to Guangzhou, this is what I would do:

Get a decent hotel in Kowloon for overnight. Next day (mid-morning or mid-day), taxi to Hung Hom station and take the Intercity/Through Train direct to Guangzhou-East. The end.

One can see plenty of highrises of Shenzhen from the train, which is probably enough for her. And for you. It's "multi-cultural", but 40 years ago, it's all fields and a small village. Hardly any history or real local culture.

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To answer your questions more directly. You're correct. Once you enter Hong Kong, you cannot use the ferries from HKG to China/Macau. Second, you can get a private van to go across the border to Shenzhen, which is not that expensive. Third, crossing the border with the regular crowd via land crossing (i.e. Shenzhen Bay, Huanggang, Lok Ma Chau or Lowu) is not pleasant, even for able-bodied locals. Doing it with a 87-year old and unfamiliar with the places is foolish, if not a bit reckless, in my opinion.