ToElementMesh of Region with Hole

I don't know why on earth a Tetrahedron-wrapped list of 3D-simplices is returned by RegionDifference, but this helps to circumvent it:

R1 = BoundaryDiscretizeRegion[
   Cuboid[{0, -wd/2, 0}, {Len, wd/2, ht}], 
   MaxCellMeasure -> ∞
   ];
R2 = BoundaryDiscretizeRegion[
   Cuboid[{Len/2 - hwd/2, -hwd/2, 0}, {Len/2 + hwd/2, hwd/2, ht}], 
   MaxCellMeasure -> ∞
   ];
reg = RegionDifference[R1, R2];
mesh = ToElementMesh[reg]

ElementMesh[{{0., 1.}, {-0.25, 0.25}, {0., 0.125}}, {TetrahedronElement["<" 13557 ">"]}]

May I suggest using MeshTools package? It offers more flexibility and alternative solutions for generating meshes on simple geometries.

Needs["NDSolve`FEM`"];
Len = 1;(*length*)
ht = 0.125;(*height*)
wd = 0.5;(*width*)
hwd = 0.25;(*hole width*)

region2D = RegionDifference[
   Rectangle[{0, 0}, {Len, wd}],
   Rectangle[{(Len - hwd)/2, (wd - hwd)/2}, {(Len + hwd)/2, (wd + hwd)/2}]
];

Needs["MeshTools`"];
mesh2D = SmoothenMesh@TriangleToQuadMesh@ToElementMesh[
    region2D,
    "MeshOrder" -> 1,
    MaxCellMeasure -> {"Length" -> 0.1}
]

mesh2D["Wireframe"]

mesh3D = ExtrudeMesh[mesh2D, ht, 5]

mesh3D["Wireframe"["MeshElementStyle" -> FaceForm@LightBlue]]