On one hand I think it kind of sucks to so heavily restrict people on when they are allowed to engage in the game's mechanics. For example, what about people working the night shift who may have more time in the morning or contractors who may have more free time on weekdays?
On the other hand, this is definitely an issue and is being deliberately misused. On NA1, there have been times when guilds have taken a port, then set the timer to the early hours of the morning specifically to avoid being attacked. Often, the guilds doing this aren't even active during those hours, but they know how slim the odds are that people will show up en masse at 4AM so they gamble on it and the game rewards them for doing so.
There's also the issue of players being on servers in regions they're not actually based in, which allows them to nearly guarantee that they won't lose a port taken at the start of the season.
Obviously, this isn't necessarily the fault of the players. The lack of an Asia server right now forces people to jump to EU or NA despite having very different active times. However, the way the port battle mechanics currently work means that people doing this would be incentivized to remain on the non-local servers and continue using timezones to gain an advantage even if local servers are initiated. Why hop from the RU server to NA or EU to Asia if the difference in time zones gives you a competitive advantage that would not exist on your local server?
I think the simplest solution is to impose harsher limits on the options for port battle window settings based on the local time of the given server.