The short answer to your question is yes, a single parcel can have multiple layers of zoning or be divided into multiple single-layer zones.
What's potentially unique about your property is the fact that you have been operating as a restaurant since 1954, likely before the current zoning was put in place. This means that you are allowed to continue using your land as a restaurant even though it doesn't conform with the current zoning scheme. Consult an attorney to double-check this.
However, this only gets you so far because once you renovate or try to expand the use or other aspect of your property, then the new rules can be applied to the new construction/renovation or what have you. Not all changes to your property will trigger application of the current zoning. It depends on how significant the renovation/remodeling is. Generally speaking you can perform maintenance on your property without triggering the new zoning provisions, but you can't expand any structures or change the use of the property. For example, you could replace leaky pipes without having to get conform to the new zoning codes, but you could not construct an outdoor veranda to host concerts or other events.
Building new bathrooms might cause the new zoning provisions to apply since it might constitute an "expansion" of the existing structure. This is something you would want to consult a local land use attorney about. If it does constitute an expansion, then you would have to go through the process of gaining approval under the current zoning standards. This could be costly and time-consuming but local planning officials generally want to support the renovation and expansion of local businesses, especially ones that have been around for a long time and have become landmarks in the community.
This is NOT legal advice, just a general discussion of the law, as we are not familiar with the specific documents and facts of your case, etc. Please consult with a competent attorney in this area of the law for specific legal advice regarding your particular case, as the advice may vary depending on the facts.
Zoning laws can be complex. Unfortunately, when people find themselves dealing with zoning issues, it often does seem unfair. There may be a possibility for you to apply for a variance. You should check with a Texas zoning attorney to see if that is a possible avenue for relief.