Everywhere that shows ship hull values at level 50 AND level 60 is actually showing the level 49 value instead of the level 50 value. In cases where lockbox ships show values for level 40, 50, and 60, the level 50 value is once again showing the level 49 value. This includes Ship Upgrade windows and the C-Store, plus externally in dev blogs.
This is based on the stats provided in this blog:
http://www.arcgames.com/en/games/xbox/star-trek-online/news/detail/10142442
Math
Formula: <Actual Hull> = <Mod> * (10000 + (500 * <Ship or Character Level>))
Mods: | 1.250 | 1.500 | 1.275
Blog L40: | 37,500 | 45,000 | 38,250
Blog L50: | 43,125 | 51,750 | 43,987
Blog L60: | 50,000 | 60,000 | 51,000
Level 40: | 37,500 | 45,000 | 38,250
Level 41: | 38,125 | 45,750 | 38,888
Level 42: | 38,750 | 46,500 | 39,525
Level 43: | 39,375 | 47,250 | 40,163
Level 44: | 40,000 | 48,000 | 40,800
Level 45: | 40,625 | 48,750 | 41,438
Level 46: | 41,250 | 49,500 | 42,075
Level 47: | 41,875 | 50,250 | 42,713
Level 48: | 42,500 | 51,000 | 43,350
Level 49: | 43,125 | 51,750 | 43,988 <- Displayed L50 Values
Level 50: | 43,750 | 52,500 | 44,625 <- Correct L50 Values
Level 51: | 44,375 | 53,250 | 45,263
Level 52: | 45,000 | 54,000 | 45,900
Level 53: | 45,625 | 54,750 | 46,538
Level 54: | 46,250 | 55,500 | 47,175
Level 55: | 46,875 | 56,250 | 47,813
Level 56: | 47,500 | 57,000 | 48,450
Level 57: | 48,125 | 57,750 | 49,088
Level 58: | 48,750 | 58,500 | 49,725
Level 59: | 49,375 | 59,250 | 50,363
Level 60: | 50,000 | 60,000 | 51,000
I do not know if this actually affects the ships, or is just a display bug.