It seems like there are two questions here, which I will try to cover fairly.
A "heavy box" probably counts as equipment, unless it's too heavy to carry.
Generally, if I can have it in my inventory without dragging it, I consider it a piece of equipment. PCs regularly carry around 65lb plate armor, and Encumberance rules go ridiculously high (off the top of my head, some PCs could carry something like 300lbs of stuff for hours without taking exhaustion levels).
This means that while the rest of the table may have agreed with the ruling that this box was special and didn't meld into the Wild Shape form, the rules as written don't bear that out.
When you want to tell the players "No", don't say No: put challenges in their way.
Your other, more social, question is about whether you did the right thing by making this ruling. You mention that the player was "quiet for the rest of the night"; they may have felt that the fun of playing a druid - which they were in a sense entitled to, by choosing to play one - was stolen from them.
You cannot control how a player reacts to a contrary ruling, but as DM, you are also responsible for "reading the room", and playing to it. I sympathize with your position here, as someone who often must say "No" to a rowdy cast of characters. But, when I do refuse them something, it isn't by flatly stating "that doesn't happen", it's by introducing a complicating circumstance in-game.
The Art of the "Yes, And"
A lot of what you're doing at a table is improvisational acting. Therefore, the "Yes, and..." rule applies. In brief: within limits, what the players say happens, happens; but the consequences of what happens are up to you.
Given your druid-and-a-box example, the most obvious "Yes, and" that I can think of is this: "Sure, you grab the box and wildshape into a rat. On your way down the hall into the kitchen, you are accosted by the biggest, meanest, ugliest cat you've ever seen, and he looks at you with his one remaining eye and says in Beast Speech: 'Prince Mittens hungers.' Roll initiative."
The social benefits of Yes-and are immense, because nobody closes out the night feeling like their fun has been stymied, when at heart they are just sitting at a table with some friends trying to have a good time. When you make rulings and narrate the consequences of actions, very often you'll find that a short-term bending of the rules, for the sake of a player's fun, can reap huge long-term benefits. Just... try not to bend rules in a way you'll regret later.
How can you tell the right and wrong ways to bend the rules? Well... that question takes a lifetime to answer :)