1) Two full technology research required...
So, to be honest it's enough to check who has more than xxx points. If a person registered 2 weeks ago has zero score points that's enough to think the village is abandoned and should be deleted
On the other hand if someone log in sometimes just to keep their account alive isn't much contribution to the neighbourhood. I see no difference between inactive 'active' player and abandoned village in my hood. I think that's another reason to support the idea of 'holiday mode'. Isn't it better to put the person in holiday mode, and if the period is longer free their position on the map - that makes more sense than login only for the fact of login.
2) Clogging Up Server
To be honest not the amount of players is the real issue. Every player is stored in a database where are few tables, for example one to store their town development (buildings type, level, position, current state...), other table store info about social activity and yet another is used to store login data. As it is relational database the amount of data mainly depends on players activity which means inactive players don't use much data. Storing for example a lifetime login data makes no sense, so if you go into holiday mode, this data (after mods check) can be deleted or archived.
So where's real problem?
Have you checked the json data produced by game and sent to your browser? If you visit another player you can see a lot of unused data, like requirements or actual production (eg 74 supplies and name of the resource: 'Bread'). It may be of use in some other game of InnoGames to plan plundering, but generally fetching all data from the database while you display just a small part of it makes not much sense. Excessive use of database and network bandwidth isn't that much related to amount of players, but it is greatly affected by amount of unnecessary data that is processed.
What I see they use separate table to store buildings data, so if 100 people goes on holiday and they have average 100 buildings (including roads and expansions) has it really that big impact on the database?