I would imagine if you are like most, you want to get the maximum from WordPress. I think most of us ask too much really. I know I can go several layers deep with one WordPress install. However, this is not really a problem so long as you adhere to good file management.
By several layers deep, I mean stack software or programs or landing pages or squeeze pages or what-have-you on top of your WordPress Install. As I stated you really will have no issues as long as you keep things straight in the directory and back-up whatever it is that you are doing. Where the trouble begins is when you try to stack everything within one database.
As far as relational databases are concerned, stacking or loading everything within one database is not really a problem either, until you have to move something or you have a technical issue with which you find yourself having to deal with.
Finding the problem is only part of the challenge, having to resolve the issue is the other side of that equation. I’ve dealt with some pretty obscure computer issues in my day, however, nothing quite takes the cake like having to deal with a specific database table, or having to export this or import that table to repair or otherwise replace.
Speed is everything Online and the last thing you need is to have a database issue that takes you done for a couple of days while you tear it apart trying to find the issue. For myself, if I tie anything to my WordPress installs I use “SEPARATE DATABASES”!!!!! That way if you ever have an issue with your programs or software you can just dump your database and re-install or rather import …… that is is you have taken the proper precautions and made back-ups of each of your databases.
If you should ever suffer a failure, you will just have to deal with one area of your Blog or WordPress Install. I’m afraid that this is not the advise of many. You will see countless articles on how to merge this or that program or software with your WordPress Database. In the immortal words of Sir Nike …… “JUST DON’T DO IT” Use separate databases for everything you do!!!!! You’ll be glad you did.