It sounds like you have the power when you need efficient data management with features that the current Zend environment doesn't work with. Zend does not have a built-in mechanism for working with databases of any type, it just has wrapper classes that help you write your queries.
You need a relational object model (ORM), which is mandatory in a professional environment. As far as I understand, ORM is a structure in itself, it has templates and clearly defined ways to "do something", supports lazy loading (it makes the most of it) and optimizes your queries to the fullest. When you use ORM, you don’t even write SQL, instead you need to change the interpretation of the data warehouse, you need to forget about tables and focus on objects. In the Doctrine, for example, each type (table) is defined by the class and each record (row) as an instance of the class, where you have access to various methods and properties. It supports event listeners and crazy cascading relations.
You no longer need to extract rows from related tables when deleting records (this is automatic), you no longer need to write complex and chaotic scripts to ensure file system synchronization, you can transfer it to almost any db engine (mysql, postgresql, simplesql ..) at any time and much more..
I am using Doctrine 2 with the Symfony 2 framework, and I must say that I will not return to Zend for anything. Yes, it is a difficult and difficult, but really the final decision. When you come to the point where you need to manage hundreds of tables with millions of total records - then you will see the difference.
So, the final summation: ORM is what you need, there are many solutions, I know two really good ones: doctrine 1 or 2 and Propel.
PS: ORM is an independent part of your system, so you really do not need to use a specific structure, Zend can be configured to work with Doctrine wonderfully :)