Solution
Deleting or removing one of the Option/Values on a Custom List used as a Matrix Option List on Matrix Items is not yet possible in NetSuite. As an alternate solution, Options may be inactivated instead. To do this:
1. Go to Customization > Lists > Records & Fields > Lists
2. Open Matrix Option List
3. Under Values tab > mark the Inactive checkbox for the Option that needs to be removed.
4. Click Save
5. Result: Record successfully saved
6. Go back to Parent Matrix Item record
7. On View Mode, under the Accounting tab, the option is still available
8. Click Edit button
9. Go to Accounting tab > Matrix Items subtab
10. Result: The deactivated Matrix Option is no longer available.