For many years now, I have handled that by writing my own. For the right applications, you can use your favorite programming language and "simply" restrict yourself to working on named cells and cell arrays (instead of all the possible data structures that are normally available.) But - of course - that leaves you having to re-implement spreadsheet features on your own. When it's a long life program, that's still worth it.

CPAN has a few modules in these general directions... Spreadsheet::Engine, Spreadsheet::Perl, Spreadsheet::Edit - some independent, some acting on a spreadsheet file.