I simplified the posted program in order to track the error. It seems that it comes from this part:

######################################

    for site in lead2.sites():
        (x,y) = site.tag
        if str(site.family) == "<Monatomic lattice e0>":
            lead2[c(x,y),a(x,y)] =1
        if str(site.family) == "<Monatomic lattice e1>":
            lead2[d(x,y),b(x,y)] = 1

######################################

I could not go deeper to find the source of the error.

The simplified program which shows the difference between"norbs=None" and "norbs=1" is pasted below:

import kwant
from matplotlib import pyplot
from math import pi, sqrt, tanh, cos, ceil
from cmath import exp
import numpy as np
import time
import textwrap as tw
sin_30, cos_30, tan_30 = (1 / 2, sqrt(3) / 2, 1 / sqrt(3))


def create_system(N=31, Norbs=None ):
   



    def rectangle(pos):
        x,y = pos
        if (0 < x <= 0.4*6.5) and (-3<= y <= 3):
            return True
        return False


    def lead_shape(pos):
        x, y = pos
        return  - 3 <= y <= 3
   
   
    graphene_e = kwant.lattice.honeycomb(a=1,name='e', norbs=Norbs)
    graphene_h = kwant.lattice.honeycomb(a=1,name='h', norbs=Norbs)
    a, b = graphene_e.sublattices
    c, d = graphene_h.sublattices

    sys = kwant.Builder()

   
    sys[graphene_e.shape(rectangle, (0.5, 0))] = 0.3
    sys[graphene_h.shape(rectangle, (0.5, 0))] = -0.3
    sys[graphene_e.neighbors()] = -1
    sys[graphene_h.neighbors()] = 1



    # Symmetry of the left and right leads
    sym_l = kwant.TranslationalSymmetry((-1, 0))
    sym_r = kwant.TranslationalSymmetry((1, 0))



    lead0 = kwant.Builder(sym_l) # Left electron                                  
    lead0[graphene_e.shape(lead_shape, (1,1))] = -1
    lead0[graphene_e.neighbors()] = -1

   
    lead1 = kwant.Builder(sym_l) # Left hole                                                                                        
    lead1[graphene_h.shape(lead_shape, (1,1))] = 1
    lead1[graphene_h.neighbors()] = 1    


    lead3 = kwant.Builder(sym_r) # Right electron      
    lead3[graphene_e.shape(lead_shape, (1,1))] = -0.3
    lead3[graphene_e.neighbors()] = -1  
 

    lead4 = kwant.Builder(sym_r) # Right hole                                                                                    
    lead4[graphene_h.shape(lead_shape, (1,1))] = 0.3
    lead4[graphene_h.neighbors()] = 1  


    lead2 = kwant.Builder(sym_r) # Right superconducting
    lead2.update(lead3)
    lead2.update(lead4)

    # Hopping between electron and hole lead lattices in superconducting lead
    for site in lead2.sites():
        (x,y) = site.tag

        if str(site.family) == "<Monatomic lattice e0>":
            lead2[c(x,y),a(x,y)] =1
        if str(site.family) == "<Monatomic lattice e1>":
            lead2[d(x,y),b(x,y)] = 1
   
    # Attaching the left electron, left hole and right superconducting lead
    sys.attach_lead(lead0)
    sys.attach_lead(lead1)
    sys.attach_lead(lead2)

    return sys, [lead0, lead1, lead2]


def plot_conductance(syst, energies, lead_in, lead_out):


    data = []
 
   
    for energy in energies:
       
       
        smatrix = kwant.smatrix(syst, energy)
        data.append(smatrix.transmission(lead_out, lead_in))
     
       
    pyplot.figure()
    pyplot.plot(energies, data)

    return data



def main():




    #case 1
    sys, leads = create_system(Norbs=None )

    sys = sys.finalized()
    kwant.plot(sys,fig_size=(20,20))

    Es = np.linspace(0.0001, 2.00, 10)
    data = plot_conductance(sys, Es, 0,1)
   
    #case 2
    sys, leads = create_system(Norbs=1 )

    sys = sys.finalized()
    kwant.plot(sys,fig_size=(20,20))

    Es = np.linspace(0.0001, 2.00, 10)
    data = plot_conductance(sys, Es, 0,1)
   
   

if __name__ == "__main__":
    main()