Shipping Wars, also known as Ship-to-Ship Combat, have nothing to do with naval warfare (or space warfare for that matter).
Many fans ship. Some of them have a distinct ship that they like over all others, while some of them support several, sometimes contradictory, pairings. Some of them like to debate a pairing while keeping in mind its status in canon, while some of them discuss it believing their pairing is canon (or will inevitably be). Now throw in the power of the Internet to connect everybody (and everybody's opinions) with everybody else...
Shippers tend to become emotionally invested in their pairings, and Internet shipping discussions can be quite difficult to keep peaceful. All too often, they can't help but devolve into heated quarrels where preferences are insulted and ad hominem attacks are thrown.
These Flame Wars are known as Shipping Wars: verbal arguments between people with different opinions about romantic relationships between fictional characters. There are those who bash whoever doesn't like their ship of choice, those who bash whoever likes a certain ship, and those who do both, usually basing their attacks on how canon/Fanon the discussed ship is. The fact that most ships really aren't canon and will never be is usually ignored.
On one hand, lots of fans see subtext, hints, and evidence where there really isn't; on the other, if there is some degree of subtext, other fans will adamantly refuse to see it and insult those who do.