A simple way, is to just iterate through the fasta file using Python and add the headers to a dict, if you find a match while iterating to the key then you can just add another field. Something like this.

from Bio import SeqIO
import os 

fastadir = ""
fastafile = "input.fa"
outfile = "ouput-editedIDs.fa"

os.chdir(fastadir) 
headerName= {} 
with open(outfile, 'a') as newFastaFile:
    for record in SeqIO.parse(open(fastafile, 'rU'), 'fasta'):
        record_id = record.id
        record_seq = record.seq 
        if record_id not in headerName: 
            headerName[record_id]= 0
        else:
            headerName[record_id]= headerName[record_id]+1
            print (headerName)
            record_id = record_id+ " "+str(headerName[record_id]) # if the header is in then we have duplicated fasta headers 
        record.description = "" 
        row = str(">"+ record_id+'\n'+ record_seq + '\n')

        newFastaFile.write(row)
newFastaFile.close()
print ("FINISHED WRITING TO FILE ")

awk '/^>/ {printf(">%d %s\n",++N,substr($0,2));next;} {print;}' input.fa