Can I get my house assessed with my rebuilt deck not up to code
That should not be a problem at all, particularly since your construction is in process with a permit. The most likely effect would be a lowering of the assessment based on an estimate of what it would take to get it up to code if you stopped construction at this stage, and railing plus finishing touches shouldn't add all that much.

Technically you can even sell a house that not only fails code in a few items but is even unable to be occupied (e.g. major plumbing problems or structurally unsafe) though obviously an assessment in such a case would be quite a bit lower. An assessment is not a code review (neither is a home inspection which gets into far more detail than an assessment), it is just a professional estimate of value based on comparable homes and the general attributes of your home.