$ cat file
"COL1"|"COL2"|"COL3"|"COL4"|"COL5"
"A1"|"B1"|"C1"|"D1"|"E1"
"A2"|"B2"|"C2"|"D2"|"E2"
"A3"|"B3"|"C3"|"D3"|"E3"
1)
$ awk '{printf "\"%s\"|%s\n", NR==1 ? "ID" : NR-1, $0}' file
"ID"|"COL1"|"COL2"|"COL3"|"COL4"|"COL5"
"1"|"A1"|"B1"|"C1"|"D1"|"E1"
"2"|"A2"|"B2"|"C2"|"D2"|"E2"
"3"|"A3"|"B3"|"C3"|"D3"|"E3"
2) reorganize a saída de 1)
$ awk '{printf "\"%s\"|%s\n", NR==1 ? "ID" : NR-1, $0}' file |\
awk 'BEGIN{FS=OFS="|"} {print $2,$3,$1,$4,$5,$6}'
"COL1"|"COL2"|ID|"COL3"|"COL4"|"COL5"
"A1"|"B1"|"1"|"C1"|"D1"|"E1"
"A2"|"B2"|"2"|"C2"|"D2"|"E2"
"A3"|"B3"|"3"|"C3"|"D3"|"E3"
2) ou diretamente do awk
$ awk 'BEGIN{FS=OFS="|"} {print $1,$2,NR==1 ? "ID" : "\""NR-1"\"",$3,$4,$5}' file
"COL1"|"COL2"|ID|"COL3"|"COL4"|"COL5"
"A1"|"B1"|"1"|"C1"|"D1"|"E1"
"A2"|"B2"|"2"|"C2"|"D2"|"E2"
"A3"|"B3"|"3"|"C3"|"D3"|"E3"