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I'm assuming you're referring to this.
The only two sections in the limitations table that require manual input are "Special Upgrade" and "Spirit Weapon". Every other box is automatically done by the itemdb fillout (meaning they will not be unknown; they are known).
Because of how the template works (the list of items that can be egoable/special upgradable is integrated into the template, rather than each weapon's data), replacing "X" by default with "?" would replace ALLLLLLLLLLLLLLLLLL "X"'s for those two sections with "?". For every of those pages, you'd have to them respecify that they cannot be specialupgraded/ego'd (redundant enough as it sounds).
Considering most items that cannot already be ego'd or special upgraded will probably never be ego-able or special upgradable, it's safe to assume all items that are not listed in this template are not egoable or special upgradable.
If, in the future, there comes a time where a currently existing item becomes egoable or special upgradable, it will quite easy to determine. All you'd have to do is look for a new itemdb entry with "Spirit ASDF" or "ASDF R/S". That would be easier and quicker than having to go through every single weapon page and explicitly define the weapon as "not egoable" or "not special upgradable".