I've skimmed every card and haven't seen an explanation, so I figured I'd ask another question.
Opp ships and SF Ship Panels can obviously have a [W] or [D] value go down to zero. To me, it's more obvious that that particular energy type is at zero if there are no chits on it at all - if I see a chit on it from across the table, I'm likely to assume that there's at least 1 energy there. I have found no techs with energy values of zero, and no boosts or missions or effects that reduce the energy of a tech to zero without scrapping/recycling it.
So...are the chits with 0 on them supposed to represent 10 energy? Or are they there to truly mean 0 for people who like having a chit in place with no value?
It is meant to explicitly show 0, instead of having nothing there. Personally, I don’t put on chits unless the value is different than the starting value. So, 0 is important.
Really? I briefly considered that but thought that couldn't possibly be the answer to why there are "0" tokens. As soon as you lay out a ship, you're supposed to add tokens to it equal to its starting value, so that starting value is only useful that one time. After that, the number of tokens shows you the ship's values, and if it has zero tokens, the number is obviously zero. I'm certainly not going to add a token to explicitly say "0" when the absence of tokens says the exact same thing.
I figured the "0" had to represent 10, and they'd just made a bad design decision in not shrinking the font slightly to allow room for a "1" next to the "0".
I think it's crazy to put tokens on every ship as it comes out. There can be far too many ships out and moving them is way harder. It's far more manageable to only add chits as the values change (your ship panel being the only exception)
OK, but that's not how the rules says to play it, and the "0" tokens must have been added to the game to support the rules as written, right? So, houserules aside, what's your theory for how the designers expected players to use the "0" tokens? It's a bit of a mystery, no?
I only put tokens on an opposition ship when it diverges from printed value, but when I put tokens on, I put them all on, so if a ship has no defense tokens, it has 0 defense. I thus never need the 0 tokens, since if a ship has no tokens, it either just got destroyed and I am in the process of awarding bounty and scrapping it, or it is still at starting values.
I do the same thing. I suppose the idea might have been that people would want to put a 0 token on when one value or the other reaches 0, but I would find this more confusing than helpful.
I don't see anywhere in the rules to suggest you're "supposed to" put tokens on opposition ships when they enter play. It's really annoying to move ships around with tokens on them, so the fewer the better.
When I play, if there's no tokens on a corner of an opposition ship, that's the current value. So I use the zero tokens to represent zero. It works well.
All of the different ways seem fine, but may make for interesting times when people who use different methods play together =)
In the one game I've played (though this number will finally go up in a couple of hours ;)), I put tokens on the card for the main Opposition ship, but never on any of their other ships unless they gained or lost any without being destroyed in the process. Thus, if a ship had tokens on it, it meant it had been buffed/damage to something other than its starting value. So, basically I do the same as pretty much everyone else here :D. I wondered about the zero-tokens as well, and wondered if they were supposed to represent tens (as a zero on a d10 does), but figured that that would be silly as they could actually have just printed a "10". I contemplated using dice, wondering if that would be easier than using tokens (as we do in Sentinels), but there ended up being a lot more ships out than there usually are targets in Sentinels so I wasn't sure. Might give it a try, though, until I run out of dice ;).
We had another game earlier and tried it with dice, putting dice onto Opposition ships when they gained/lost any shields/weapons to alter them from their starting values, except for the Flagship, which just got dice as soon as it flipped. All Strike Force stuff just got dice all the time. Ran out of d6s and d8s at one point (I only have five of the latter) as the Opposition was putting out a lot of stuff (Technovores) and one or two Sectors and Missions did quite a lot of "all the ships lose energy" effects, but we did okay.
And we won :D. I'm hoping we did everything right. Bjarlspire and Uxshenti's Wrath versus the Technovores. He tanked, I pinched a load of guns and nuked stuff, eventually we took on the giant spider and blew it up in the Battle Phase of the same turn which would have seen the final Sector overrun had we got to the Aftermath phase. Phew.
Yeah, the 0 tokens are for indicating when a ship has 0 W or D, which is key when dealing with Opposition ships. I get that not everyone will use them, but I know I use them!
I like that they're there for folks to use if they want. Same with the condition indicators for SotM - I know a lot of folks don't us them, but others find them invaluable. As long as we play the game and GtG provides us with tools to support the game (use them or not), I'm happy! 
Dont put tokens on ships until the value change and you will divide by 2 the fiddleness of the game, have a nice, large box for tokens on hand and it gets down to decent fiddling. Not putting token until it change make also for more readable combat value from afar.