Wiring – How to connect multiple ground wires in this case (replacing ceiling pendant lights)

Both black and red are typically used to indicate hot. Though you can't be positive without actually testing it with a multimeter. Red is usually used when there are two hots (14/3 wire instead of 14/2).

Both green and bare copper are used to indicate ground.

So it sounds like you wired it correctly. The green wire from the line (source) should also be attached to the green grounding screw in the electrical box.

The silver wire is also a ground. Chains are not grounding paths so a pendant needs 2 grounds - one down the chain to the pendant, and the other for the box cover.

I suspect the manufacturer ran an extra run of 14/2 (12/2?) Romex from the switch to support a ceiling fan which you don't have (yet). I bet the third black is folded up in the back of the box, but they tied this pair's white wire with the other white wires. That's making my spider-sense tingle, but I can't say why. Might make a good question.

Since the power is fed from the switch (no weird switch loops) you should be able to connect all blacks to each other, ditto the whites. All grounds must be connected together. I don't see any obvious way that upper steel plate bonds to the maze of ground wires above it, and that makes me a bit nervous. Is that a steel box above, and is the ground bundle bonded to it in some way? I see a screw, but it's not green and may be a physical mounting. Is the steel cover plate tightly screwed to the steel box?

As far as wire-nuts, each make of wire-nut is listed for certain combinations of wire. For instance Ideal's 73B (orange), 74B (yellow) and 76B (red) are covered in a document titled UL Listed wire combinations... Generally I like to be in the middle of the working range for a wire-nut, so I'd go yellow for 3 wires, red for 4, and orange for something that seemed on the smallish range for yellow.