The standard numbering most used is MIL-STD hardware. For instance MS6995-9 is a 4-40 x .25 300 series stainless socket cap screw. Then there are modifiers for material and finish. Using MIL-STD hardware will usually drive up cost a bit, because even though it is the same hardware, there are documentation requirements.
The standard that won't drive up your cost is ASME B18. This is much less common, but hardware vendors will be familiar with it.
Also, CAD companies don't standardize o-rings and snap rings. SAE does.