Bash/awk

#!/bin/bash

declare -A T2 T3; declare -i S1 i=0
while read DATE X  ; do
        T1[((i++))]=${DATE:0:8}; T2[$DATE]=$X ; T3[${DATE:0:8}]="ok"
done < fichier_dates
S1=$(date -d "${T1[0]:4:2}/${T1[0]:6:2}/${T1[0]:0:4}" +%s)
D3=${T1[0]}
while [ $D3 -le ${T1[((i-1))]} ]; do
        if [ -n "${T3[$D3]}" ]; then
                for n in {00..23}; do echo $D3$n ${T2[$D3$n]}; done;
        else
                for n in {00..23}; do echo $D3$n -999; done; fi
        S1+=86400
        D3=$(date -d "@$S1" "+%Y%m%d")
done

$ cat  f2
#!/bin/bash

declare -A T2 ; declare -i S1 i=0
while read DATE X  ; do
	T1[((i++))]=$DATE; T2[$DATE]=$X
done < fichier_dates
D1=${T1[0]} ; D2=${T1[((i-1))]}
S1=$(date -d "${D1:4:2}/${D1:6:2}/${D1:0:4}" +%s)
D3=$D1
while [ $D3 -le $D2 ]; do
	echo -n "$D3 "
	if [ -z ${T2[$D3]} ]; then echo -999; else echo ${T2[$D3]} ; fi
	S1+=86400
	D3=$(date -d "@$S1" "+%Y%m%d")
done

$ ./f2 
20001212 5
20001213 -999
20001214 -999
20001215 -999
20001216 -999
20001217 -999
20001218 -999
20001219 -999
20001220 -999
20001221 -999
20001222 -999
20001223 -999
20001224 -999
20001225 -999
20001226 -999
20001227 -999
20001228 5
20001229 4.3
20001230 25.2
20001231 32
$