Negative values are intended and the math should work, but let me know if anything looks off. The Broadsword and Tower Shield have negatives to Agility. Inherent stat growth and rare items may eventually offset the penalty, but the trade for the much higher defense / damage output is that you may not hit or dodge as frequently.

The main quest can be completed with just a short sword and a heater shield, as long as you're diligent about upgrades / leveled properly, but it'll be slower or more challenging. The additional weapons and shields let you play with your stats in a way that may let you do some paths earlier or make a build that is more suitable to how you want to approach a battle.