VK_CLEAR has been present in Windows headers since Windows 1 (it's listed on page 57 of the Windows 1.03 SDK documentation, for example).
Windows 1 could run on, among other computers, the Apricot PC, Xi and Xen. These computers had a dedicated Clear key, and so it is possible that the
VK_CLEAR code was created to support the keyboards on these computers. Once Windows supported
VK_CLEAR, it would be reasonable enough to map an otherwise unmapped key on the PC / XT / AT keyboards to it.
Looking in windows.h (WinUser.H in 32-bit SDKs),
VK_CLEAR is defined as 0x0C. This is part of a group with
VK_BACK = 0x08,
VK_TAB = 0x09 and
VK_RETURN = 0x0D. That suggests an intended association of
VK_CLEAR with the ASCII 'form feed' character, Ctrl+L, which often clears the screen in terminals and terminal emulators.