First off you only need to keep 1/4 of what it costs for a toon. The shop refreshes 4 times a day, and if you do GW daily you get enough to buy a toon 3 times out of 4. So to farm a new toon as quickly as possible all you need to have saved is 6,600.
However I wouldn't blow through it all to turn into shard shop currency because you can do that in 2 days. Yes, if you have every toon and ship at 7*, then you can buy 6 rows of 3 at 400 a pop. That's 7,200 currency you can convert 4 times a day without spending crystals to refresh. 50,000 won't take long to convert doing 28,800 per day. And I've never seen a toon fly through the shard shop in less than 2 days.
In conclusion... just sit on it. It's not hurting anything where it is. It can rapidly be converted for the shard shop if need be. But you can't un-spend it once it's done. And you never know when some new feature, or use for it might come along.