Honda made pretty strong and durable engine that stands up to most abuse pretty well. Neglect isn't an abuse well tolerated, though. If you want to buy parts for rebuild in 15yrears, that will add legs to the bike's life. But, with 9K miles the engine, it is just past the break in point. Take the head off if you must, But I think you should have run it another 100-200 miles to see if it would all seal itself up again after doing some real work rather than just sitting.
Kinda depends on why the comp was low on one cylinder. But, my 77 CB550F sat for 15 years. Had 8K miles and low compression on one cylinder, so I only paid $100 for it. I did the usual to make it run again, but never opened the engine, and 100 miles later all the compression checks came out equal. In fact, that thing seems to have more power than all the rest of my 550s. I don't buy the "while-I'm-in-there" snowball effect at rebuilding. It's a waste of time, money, and effort most times. imo.