Downsides/overuse of tables?

I'm working on a batch processing software that can often involve similar kinds of information that need to be slightly modified for different file types, conditions, or modules. I've found that using tables is incredibly convenient in these circumstances, but have started to notice myself relying on them frequently when information overlaps in these ways. Is there any downside to this that I'm unaware of? Trying to make sure I don't fall into bad habits.

Examples of tables I currently have:

1. User inputs: Rows are modules, columns = Module On, Module Export, Module Report etc

2. File information tables, pointed to by user: 4 different kinds depending on usage. For a typical table, rows=files, columns = information of various types about files

3: File processing information for modules of different types (4 kinds): In one case, rows = type of data analyzed, columns = analysis types used in different modules. The values in this case specify the range of values included for that type, in that module. In another example, user flagging of variations of one analysis contained in one of the modules in the user inputs, which allows me to vectorize the applied analysis rather than having one giant if-else statement or switch.

4. Storing local condition information, which is pulled from files about the environment and includes names and values for a given environmental variable. All files have this information, but it's never the same across files.

Thanks in advance!