(1) 解:如图①,连接$OB。$因为$OD\perp BC,$$BC = 4\sqrt{3},$所以$\angle OEB = 90^{\circ},$$BE = \frac{1}{2}BC = 2\sqrt{3}。$
设$\odot O$的半径为$R,$则$OB = OD = R。$因为$DE = 2,$所以$OE = OD - DE = R - 2。$
因为$BE^{2}+OE^{2}=OB^{2},$所以$(2\sqrt{3})^{2}+(R - 2)^{2}=R^{2},$
展开得$12+R^{2}-4R + 4 = R^{2},$
移项得$R^{2}-R^{2}-4R=-12 - 4,$
合并同类项得$-4R=-16,$
解得$R = 4。$故$\odot O$的半径为$4。$
(2) 解:如图②,连接$OB,$$BD,$过点$O$作$OF\perp BD$于点$F,$延长$FO$与$\odot O$交于点$A,$则此时阴影部分的面积最大。
因为$OA = OB = OD = 4,$$DE = 2,$所以$OE = OD - DE = 2,$所以$OE = \frac{1}{2}OB。$
因为$\angle OEB = 90^{\circ},$所以$\angle OBE = 30^{\circ},$所以$\angle BOE = 90^{\circ}-\angle OBE = 60^{\circ},$所以$\triangle OBD$为等边三角形,所以$BD = OB = 4,$所以$BF = DF = \frac{1}{2}BD = 2,$所以$S_{\triangle OAB}=\frac{1}{2}OA\cdot BF = 4,$$S_{\triangle OAD}=\frac{1}{2}OA\cdot DF = 4。$
因为$S_{扇形OBD}=\frac{60\pi\times4^{2}}{360}=\frac{8\pi}{3},$所以$S_{阴影}=S_{扇形OBD}+S_{\triangle OAB}+S_{\triangle OAD}=\frac{8\pi}{3}+8。$故阴影部分面积的最大值为$\frac{8\pi}{3}+8。$