My first thought is as long as the thickener is compatible with the resin system, any one that approximates the hardness of the deck is fine. I could see issues with significantly more hardness in the filled holes than the surrounding deck, with differential flex it may crack and leak. Not sure if that’s a thing. You could do a test layup and see.
As for the ambient temperature and the small size of the repair, heat lamps or electric blankets can warm the surface just enough to cure the epoxy.
Boatworks today did a piece in this a while back.

 

What AWT2 said about the filler.

What's more important if you've not done this type of work in the cold, is the cold AMHIK. West epoxy in cold temperatures simply takes forever to cure, no matter how much filler you have; it will run all over the place. While AWT2's video above has some tricks, my suggestion is to simply wait- I've tried some of those tricks and it's still a challenge.

 

It is not too frigid - on work day the high will be 13C / 55F and afterwards the highs will be 16C / 70F - with our fast hardener - I am not worried about it curing.

My question was about best way to fill tiny holes - how to have the least viscous material so it fills the small holes best possible. I was thinking of using unthickened (and pre-warmed) epoxy so it flows better and fills the small 3mm holes better.

 

Oh I get it now - thanks.

 

403 if you have a choice, as stated above your big challenge is to keep it where you want it to be. Consider experimenting with the mix, see how thick you can get it and what it does on a test surface as it cures.

 

105 fast hardener is the right call, but it will still take a while to cure. 105 and heat lamps are what we use here in NC in the winter time. (our winter prob similar to your spring?)

403 is overkill but I would choose it over 407 for this. Tape the bottom of the hole if you have access to it. Use small paintbrush to prime the interior of the hole. Thicken the rest ... if you have the bottom taped it, I'd go with mayonaise consistency. if not you will need to go much thicker. Either way, air bubbles are you enemy so fill the hole and use chopsticks or similar to pack it in and get the air bubbles out. fill it till slightly proud of the surrounding surface.

for the screw holes, yes unthickened is fine. Drill out to 3mm, vacuum out the debris, pour it in, a little proud.

 

For cable glands, what I like to do is clean out the core including the cable entrance AND where the screws will go. I then tape the bottom and fill the entire hole with thickened epoxy using a glue syringe. The glue syringe makes it easy to fill from the bottom and avoid air bubbles.

 

Obviously, you can get coliodal silica anywhere civilized. There is nothing special about 406 that makes it "compatible" with West Systems epoxy. This is true of all fillers. In fact, you can do quite well filling holes by chopping up glass cloth fine and using that. Done well, it is the strongest option.