I am considering upgrading a legitimate version of 64 bit Windows 7 to Windows 10 (or possible future versions if generally compatible). These days, with ever faster solid-state drives coming along and common storage of large files and applications on another drive, is it okay to upgrade Windows without having to uninstall and re-install applications on other drives? I know their registry entries will be associated with the drive the OS is currently installed on, so don't expect any broken registry entries. I assume the process would be the same as if the applications were installed on the drive the OS is on (whether 32 or 64 bit applications). To be on the safe side, it should be possible to re-install these applications from scratch, but is a far more time consuming process. I know Windows does a good job of reporting the extent of the upgrade process to users and system changes made.
From my understanding of your question, you have two main things. One would be upgrading your main HDD to an SSD and upgrading from Windows 7 to Windows 10. Normally, if you update your Windows from 7 to 10, you should be able to do it without any problems in regards to the applications. But, since upgrading to an SSD means you have an all new "main OS drive", no one can assure you that the applications on the other non-OS drive will work flawlessly. One solution might be trying to clone your main drive to the new SSD and than update from Windows 7 to Windows 10 on that one. But to me it seems, it might be less of a hassle if you install Windows 10 on the SSD and simply try to repair or reinstall all your applications on the non-OS drive. Even with Windows upgrade process, there some settings, things, that are very hard to clone or be copied from one drive to the other.
After seeing your comment, I would say that according to this microsoft site, such an update is possible without data loss, meaning in theory, all your applications should work. All you need to do, is follow the link and download the "update assistant" windows update tool, start upgrade with that. At one point, you will be asked if you want to keep your files or not. Select to keep it and in some time, windows 10 should be up and running. It might be good keeping in mind, that even though Microsoft itself says that no data loss will occur, they advice to making a backup.