Can Ernst Sr actually disinherit Ernst Jr? For example QE11 wouldn't be able to disinherit Charles in favour of Andrew would she?
I remember that Ernst Sr had to get the Queen's permission to marry
Would this apply to Ernst Jr? in which case would whatever his father does re the succession matter?
No, that doesn't apply anymore because the Royal Marriages Act, which was the British law that required the Queen to consent to marriages of descendants of King George II, has been repealed by Succession to the Crown Act 2013.
On your second question, QEII cannot remove Prince Charles from the line of succession to the throne because the line of succession is regulated by law and the Queen cannot change the law unilaterally (she needs the "advice and consent" of the UK Parliament to do so under the British constitution !). As a private citizen, my understanding is, however, that , under English law, the Queen can leave her private property to whoever she wants, so it is not automatic that Charles e.g. should inherit Balmoral or Sandrigham alone as neither one are held in trust by the sovereign. In fact, when Edward VIII abdicated, he retained ownership of both estates, and King George VI actually had to "buy" them back from his brother under some kind of financial settlement , see
this reference . It is just customary that the heir to the Crown gets most of former sovereign's private estate, not least because asset transfers from a sovereign to another are exempted from inheritance taxes.
In the case of Ernst Sr. and Ernst Jr., one would have to examine German inheritance law to answer your question. Most continental European countries follow what the Brits call the "Napoleonic system" (after Napoleon's civil code) where children are natural heirs and assets must be divided equally among them, so I suppose disinheriting someone is not so easy as it is e.g. in English law where a legally valid will pretty much overrides everything else. I am pretty sure though that our knowledgeable German posters here will be able to explain it much better.