1) The noun is used of a fissure or cleft in timber which developed during a tree’s growth.
1686 boards without either shake or sappe or any other thing which may be thought to be hurtfull, Conistone. The condition is considered to be a defect and was so described by the Lepton horticulturist William Pontey in The Forest Pruner. Under the heading Shaken Timber he gave some credence to the view that such cracks might be wind damage but cautioned against thinking that might be the only cause. A North Riding document also gives it as a defect: a.1660 many old doterelles … decayed and shaken trees, Wheeldale. It could also refer to the harm caused by coal-getting, both underground and on the surface: 1683 the grounds are so shaken and spoyled by the undermining thereof and by the coal slack and rubbish that lye upon the same that little or no profit can ever be made, Whitkirk.
2) As a verb it could refer to the customary right of turning animals or poultry into the stubble after harvest (EDD).
c.1547 the inhabytantes of ... Saxton ... have usyd tyme owte of mynd yerely after harvest done to shake wyth theyre beastes and cattelles in the sayd too closes. Perhaps this was originally to feed on the shaken corn, the grain that had fallen to the ground: 1642 Oates are a graine that may bee cutte greener then any other white corne ... the hinder ende of them will shake afore yow can gette to mowe them, Elmswell.