解:
(1) 过点$D$作$DF⊥ AC$于点$F.$
$\because ∠ ABC=90°,\therefore AB⊥ BC.$
$\because CD$平分$∠ ACB,\therefore BD=DF.$
$\because BD$是$\odot D$的半径,$\therefore DF$是$\odot D$的半径.
$\therefore AC$与$\odot D$相切。
(2) 设$\odot D$的半径为$x.$
$\because ∠ ABC=90°,BC=3,AC=5,$
$\therefore AB=\sqrt{AC^2-BC^2}=4.$
$\because BC$与$\odot D$相切,$\therefore BC=CF=3.$
$\therefore AF=AC-CF=2.$
$\because AB=4,\therefore AD=AB-BD=4-x.$
在$\mathrm{Rt}△ AFD$中,$AD^2=DF^2+AF^2$,即$(4-x)^2=x^2+2^2$,解得$x=\frac{3}{2}.$
$\therefore AE=AB-BE=4-2x=4-3=1。$