select_near_vertices.py

import mathutils
from mathutils import Matrix
import bpy

from typing import List, Dict, Tuple, Optional

target_mesh_objects: List[bpy.types.Object] = [o for o in C.selected_objects if o.type == 'MESH' and not o.hide]
i2vm: Dict[int, Tuple[bpy.types.MeshVertex, bpy.types.Object]] = dict(enumerate((v, m) for m in target_mesh_objects for v in m.data.vertices if v.select))

mesh_object: Optional[bpy.types.Object] = None
mesh_matrix: Matrix = Matrix()
vertex_index = mathutils.kdtree.KDTree(len(i2vm))
for i, (v, m) in i2vm.items():
    if m != mesh_object:
        mesh_object = m
        mesh_matrix = m.matrix_world
    vertex_index.insert(mesh_matrix @ v.co, i)

vertex_index.balance()


import bmesh

for m in target_mesh_objects:
    mesh_matrix = m.matrix_world
    me = m.data
    bm = bmesh.from_edit_mesh(me)
    for v in bm.verts:
        _co, index, distance = vertex_index.find(v.co)
        if distance < 0.001:
            v.select_set(True)
    bm.select_mode |= {'VERT'}
    bm.select_flush_mode()
    bmesh.update_edit_mesh(me)