I'm not even a Half-Life fan, but I don't see any yellow paint... There's a diegetic yellow sticker with a barcode that says "supply." It communicates that the player should have an interest in its contents without making the signalling unnaturally ostentatious. If it were a crate released in a game today it would be covered with yellow tape for no reason whatsoever:
Why would anybody do this, let alone to every crate you find? Are we supposed to imagine that all the crates are so flimsy and poorly put together that haphazardly wrapping it in tape is an improvement?
Here's another with actual yellow paint. Notice how the yellow barcode in HL2's crate actually seems like it could serve a purpose in the world? Why would there ever be a crate with a few splashes of yellow paint on it like the above? It's completely irrational that someone would walk around with a bucket of yellow paint and a brush only to make a couple swipes on each side of the box. It's not that the developer is signalling to the player that an item is interactable, it's that they've put no thought into the manner in which they do it other than to make it stand out in the easiest way possible.
Another example of good signalling is Blighttown from Dark Souls:
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You probably won't even notice when playing the game, but every ladder has a torch next to it. You expect to see some torches around a place like this and they naturally draw your attention to the ladders without seeming out of place. Compare to a game with the yellow paint philosophy:
Need I even comment further?