Does the ICAO definition of an "aircraft" include a minimum altitude capability?
Is there a lower altitude threshold in the ICAO definition of an aircraft?

No.

Is a wing in ground effect craft an aircraft according to ICAO definition?

No.



I believe the ICAO is based on the Chicago Convention

The 2006 9th edition begins 


  THEREFORE, the undersigned governments having agreed on 
  certain principles and arrangements in order that international 
  civil aviation may be developed in a safe and orderly manner 
  and that international air transport services may be established 
  on  the basis of equality of opportunity and operated  soundly 
  and economically


Although this has a section on definitions, it doesn't define aircraft.

The ICAO ADREP taxonomy contains this definition:


  Aircraft. Any machine that can derive support in the atmosphere from the reactions of the air 
  other than the reactions of the air against the earth's surface. (Annex 
  8)


That appears to exclude vehicles whose support relies on ground effect only.



Why [was] the 100 ft threshold [...] put into the German (or other) laws?

That might be better answered in law.se