My decks are shortly approaching the point of a ship upgrade. I was hoping to keep my ship size at it's current stage for a little while. What I'm wondering is will my race bonus of '+10% ship size' count towards my ship upgrade, or will my ship size be based on the decks listed in the 'Ship Crew & Size' tab?

The deck size you see listed on your ship tab, includes the +10% ship size already.

The "Space" indicator, and the number listed in "Ship Crew & Size" are two different numbers. What I'm meaning to ask; is if the "Space" indicator, that shows the amount of available decks that can be used(after adjustment from the Sillixx 10% bonus), has any bearing on the size of the ship?

For example: When the amount of decks in the "Ship Crew & Size" tab reaches 44. The "Space" indicator - which is described as "The amount of deck space available on your ship to install modules and weapons", will be at either 48 or 49. What I'm wondering is; if the "Space" size were to be increased to 50, by bringing the amount of decks listed under the "Ship Crew & Size" tab to aprox 45 or 46. Will the amount of 50 - indicated next to "Space", cause my ship to upgrade from a Scout to a Light Frigate?

Yes it will.

It's your decks WITH the sillixx boost that will count toward that.

Also, I recommend changing race as soon as possible, because you WILL become dependent on that extra 10% size. The sooner you change the better.

One other question, if my ship happens to get upgraded by a point or two from the Sillixx bonus. Will the ship downgrade after changing my race? Like if the amount of decks listed in the "Ship Crew & Size" tab were still at 49 or 99, etc.?

When you are NOT Sillixx, the true number of decks you can use is equal to what it shows in the Crew manifest. As already stated by someone earlier in this thread, get away from Sillixx ASAP. The later you switch, the harder it becomes. You either have to uninstall equipment from your Sillixx build until you meet the unadjusted deck total, or you need to stockpile enough ship bots and/or rank points to make up the difference.

Also, the ship size it says doesn't matter whatsoever. People can see the exact amount of decks you have by looking at your medals.

This... Not sure why everybody hates on Sillix. I used it to great effect until about rank 250. Simply plan ahead and it wont cause you any trouble at all. Stockpiling isn't even necessary really, just remove non-critical modules until have the space to reinstall them.

I don't hate it. I just see it as one of the less helpful bonuses. You're better off with Konqul, Aerlen, or even Vygoid at low ranks. Konqul and Aerlen (as far as I know) never become "bad" choices.