NYC DOB considers a shelter a 'community facility with sleeping quarters' and may require a special permit for this use.Thanks Abel, You provided me with the right search terms to dig deeper. 

Does that mean I'm all set and can break it up in to separate units, or do I need to get a permit or rezone or other things?

One metric we do use when we're able to pull the data are permits pulled & what type of permits pulled in an area.

At the same time I have my current home as an asset to rent out if my HOA permits it.

Depending on the construction, you have to do major upgrades on electric, plan for plumbing for apartments which may not be permitted in the area for the sewer or septic.

I have 10 water front lots on a trout river in WNC with mountain views, they are cleared. i have the site permit, i have the well and septic permits.

No architect drawings, no permit fees.  

If they are separate, permits would have been pulled and the city will have records of those permits.  

if its only one sub it could have been an oversight. 3 years  is this because permits take so long..

It may be due to the lengthy pool permitting and construction process. 2025 will be a critical year.