I couldn't tell you the grammatical reason, but strictly the 'him' in your first sentence should be 'his'. There's not many of us who would say that, though, so if the rest of your grammar isn't pedantically correct it may stick out. In any event, I think Ursa's suggestion of changing the wording at the end is a better one, though I'd have made it:
When he stepped forward to take her hand, she noticed she overtopped him by an inch, despite the fact he wore [heeled] boots and she wore slippers.
I'd repeat the 'wore' for the sake of readability, I think. Being English I can't say 'overtopped' grabbed me, as it reads very American-ish, so if you're doing an historical-type fantasy you might want to think about it.
How you treat the second sentence depends on the context, I think, but as Devil's Advocate says, you need a 'nonetheless' or 'still' to give emphasis (though I don't think 'still' at the very end of the sentence would work except in dialogue and even then might sound odd). If the sentence is in dialogue or the narrative is written in first person, then you can get away with the rest of the wording. but I'd make it:
That [though 'It' might be better] was disappointing. Not surprising mind you: [or a long dash - I'm addicted to them!] it was typical behavior for a nobleman’s son, but still disappointing.
In ordinary third person narrative, you should avoid the use of 'you', so I think:
That [or 'It'] was disappointing. Not surprising, since it was typical behavior for a nobleman’s son. Disappointing, nonetheless.
though there are any number of variants, eg based on Devil's Advocate's idea:
That [or 'It'] was disappointing. Not surprising -- it was typical behavior for a nobleman’s son -- but disappointing nonetheless.
each of which would be punctuated properly, but would give slightly different emphasis or a different feel and rhythm to the paragraph. Read the whole para out loud to yourself to get a feel of where you want to pause and for how long, and that will give you the punctuation you need.
For general advice on punctuation, have a look at
The Toolbox, a sticky at the top of Aspiring Writers.