Do about roofing and framing nail ‘shiners’ under eaves

First concideration, I would encourage you to use a T&G roof sheathing such as AdvanTec instead of standard CDX plywood. This will give you a better fit and not have to worry about spacing gaps in the plywood. The price is comparable, so there is no cost advantage to using regular plywood.

The sheathing should be secured with 6d galv ring shank nails at apx 8" spacing. 1 5/8" coated drywall screws are great, but more time consuming to install. Don't use non galv common nails, as they tend to back out after a few years.

If your sheathing fits properly on the joists with 3/4" overlay, nailing straight down is fine as long as you bite into solid wood. A slight angle towards the joist is OK as long as the heads of the nails or screws don't protrude above the sheathing. Protruding nails can damage your roofing material, assuming you are not planning on using a layer of Grace Ice and Water shield under your final roofing materials.

Roofing nails are a bad choice for attaching sheathing. The wire gauge is too small and the hardness of the nail shank is much less than a framing nail. I personally like to use 6d or 8d ring shank nails for OSB. 8d common nails are Ok as well. Ring nails won't loosen or back out over time as wood dries and shrinks. The heads of the roofing nails can easily break off and will offer little if any holding power. Although you may save some money now, having your sheathing loosen over time will be extremely expensive to fix later. Use the right materials now and be sure the job is done right.