I mean other than the fact the citadel gets all nasty brown, does it affect anything else?
If you are asking if it affects your clan in any way, I don't believe it has any affect at all. If you are only at Tier 1, the citadel locks itself if you fail to meet the weekly upkeep, and has to be re-opened via the portal ritual.
Citadel maintenance and how much it matters to you really depends on what you use your citadel for and how much you get out of it. I know that the clan I am currently in really loves the use of Clan Avatars, and so without maintaining ever week we lose the avatars and all hell breaks loose. A dilapidated building/plot also causes the citadel to function at a lower level and you lose XP and other benefits that you would otherwise receive from the citadel.
Can you make it so you pay upkeep in a different way instead of wood?

