I think joining two guilds would affect whatever they have planned for guild gameplay. For instance, if gameplay required players in each guild to acquire items or XP to level up a guild, then it would be unfair if there was a player in two guilds who might favor one guild over the other during gameplay - leaving their second guild alone whilst the players in that second guild could be left to pick up the slack.
If leaderboards were a thing for guilds, then maybe it might mess up how points are tallied for a player in two guilds unless they can easily sort that out.
Other than that, they can probably do two guilds per player, but forcing a player to choose which guild they want to do gameplay for during the duration of guild events. Or maybe make this second guild nonexistent for any guild gameplay events.