Scooby doo didn't understand relationships, sure he understood the he was Shaggy's best friend and that the gang were his friends. That was friendship though, not a relationship. So no, he didn't understand why shaggy felt the need to be in a relationship. He did understand that whenever shaggy entered one he unconsciously abandoned Scooby, as such Scooby took any romantic intentions towards Shaggy as a threat. Yet she had captured Shaggy's heart without anyone realising and maybe that's why Scooby wasn't threatened by her. It seemed that neither lovers knew themselves.

In fact, no one seemed to know, well except Scooby's sister. Ruby Doo, she had come to check up on Scrappy, whom had turned six the week prior. Scrappy had of course been ecstatic to see his mother and had regaled her with their adventures. After a while Ruby commented on the closeness of Shaggy and Daphne, Scooby had laughed it off because they were friends and yes friends did act that close and touch that intimately. Looking back on it he realised she was right, his best friend was falling in love.

It took Scrappy's interference for Scooby to realise that Shaggy and Daphne were inching into the unknown territory of romance, all it took was for Scrappy to show his uncle that the kisses were anything but innocent.

When Shaggy started slipping away Scooby knew his best friend was lost forever and as such he began to distance himself from both Daphne and Shaggy but the girl was having none of it. She wandered in to Scooby's room and sat next to him.
"It's okay to feel scared but I promise I will not pull him away" Scooby looked at her, steely determination in his eyes.
"Rhy should I relive ru?" he asked. Daphne laughed, a cute laugh that ordinarily would have made Scooby smile.
"You do know he said we could never be, together right? He said that so long as he had you he would be content. You may think he won't want you anymore but that so wrong that I can't even tell you how wrong it is." Scooby looked down, he knew that Shaggy had been miserable lately, he didn't know why but now he did. Shaggy had chosen him over Daphne.
"Ru promise ru won't roget re?" he asked, Daphne laughed
"I promise, so would Shaggy if you asked him" it was at that moment that the lanky teen wandered into the room.
"Scoob, daph?" he asked. Scooby smiled
"I love you Raggy"
"I love you too Scoob" he replied, confused. Scooby gave Daphne a lick
"Ru two ca rate" and then he left them alone.

It took them a while to figure out their way, how Scooby fit into their family If he wasn't Shaggy's confident anymore but they made it work and Scooby never regretted letting Shaggy love Daphne because they had such a special relationship, full of love and compassion and that only continued when four years later he stood beside Shaggy as Daphne walked down the aisle. Her dress the epitome of elegance and class. He watched as Shaggy and Daphne made the ultimate vow to love each other forever and always and he smiled. He was hesitant about them, he'll admit but it was his duty as mans best friend to make sure his best friend was okay. It seemed he had succeeded.