As an active collector and participant in the secondary market and current owner of over 20 watches, I can tell you that many high end watches are sold and traded every day without certificate or box. Obviously having both is desired and preferred but the watch is the centerpiece of the purchase.
I have never turned down a great deal on an exceptional timepiece just becuase the papers and box are no longer available. Even serious collectors misplace papers and boxes over the years. In fact, on more than one occasion I've seen the wrong papers paired with a watch - the owner had more than one piece over the years and inadvertantly mixed up the "peripherals."
I recently purchased a high end discontinued "grand complication" platinum Patek that was still sealed in the original cardboard display box (the cardboard was still sealed, plastic sealed, tag, etc.). The price was fair, the watch has been untouched for years since leaving Patek but the papers and winding box have been lost. I guarantee buyers would jump all over this piece because the watch is in perfect 100% condition.
Many of the older boxes have deteriorated over the years. I owned three high end Pateks from the 1980s that are getting amazing prices today. The interior of all three of the wood boxes has completely deteriorated with flaking of the lining destroying the leather straps and making the box unusable even though they were stored in a temperature and humidity controlled environment. Does that make the watches less valuable? Not in my experience.
Furthermore, many of the extraordinary vintage pieces that have been achieving unbelievable prices at auction do not have original papers or boxes. They have simply been lost or misplaced over the years. Sure, I want the entire package but I'm not going to walk away from an exceptional watch and a good deal just because of the paperwork. And in my experience, most secondary buyers agree, as I've never had difficulty selling a piece at a fair price.