I have done this myself using BIP39 HD Wallets.
I wrote the code in C# using SQL Server for the database.

It was very hard work as most of what is out there uses non-enterprise level code such as JavaScript, GO or PHP.
Any databases they used were open source and had no consideration for security or scale.

SQL Server has built in always on encryption with enterprise level security, so a good foundation.
The way you build your API can restrict access to only the accounts that they need to access so I do not see this as an issue as far as system wide security goes.
It is only a risk to the funds of the developer holding the API key so it becomes their responsibility to look after their own keys.

Hope this gives you some clues as to where to start but HD Wallets are the future for this type of application.