Unless a mechanic has changed, I don't think you're guaranteed a starting area with the full number of villages and mana crystals unless you have every card in the game unlocked. Is this considered more valuable than having a deck without every card so you can more easily guarantee you get the draws you want?

Depends on what mode you are playing and what goals you have for that mode. If you are playing with all towers or very loose strats or easier difficulties, the full number of villages is worth more.

If you are playing endless or march, having more tower options can help you make more money since you get extra money for each unique tower hitting and you churn through more cards and you'll get more for those villages.

If you are playing Ballistas only triple or quadruple lane, then playing with a smaller deck and hoping to proc one of the tiles with villages on it is way more efficient and probable for actually winning since you basically need all the Ballista upgrades to even have a chance and wasted rounds on other towers is a setback.

So if you're playing normally, you want all of the cards - if you're going for the achievements, then it's actually more consistent to have a smaller deck?

Don't forget that most cards (certainly all towers) start cheap and become more expensive each time you play this particular type of tower. So a bigger deck also has advantages since you do not ramp up the gold price so quickly.