There will be lvl 99 upgrades for all relic/mythic/empyrean weapons.

Also, merging might work for your relic+emp great axe, but it will fall flat on it's face for mythic + emp weapons or jobs that don't have access to a relic or emp to merge.

Just try merging Kenkonken and Verethragna for instance.. besides the fact that it exceeds the maximum number of stats on an item, it also has to deal with two different aftermath effects, and MNK cannot use Kenkonken so Kenthragna would be PUP only.