If I understand your experiment, the parental strains are each homozygous mutant.  One parent produces a larger SSR product and the other a smaller.  Then yes, the F1 offspring will always be heterozygous and will produce two bands.  Now, keep in mind that PCR reactions will tend to be more efficient for the smaller product so you will not expect both bands to be equally bright.  You might have to adjust your PCR conditions to make sure you see both bands.

F1 resulting from 2 homozygous lines  is 100 % heterozygous and any codomminant marker will always show two bands. Is there specific reason to confirm its heterozygosity?

If the two crossing parents are homozygous and markers used are polymorphic, presence of both bands (each corresponding to the parent) confirms F1 plants.

Prerequisite for confirming F1 (heterozygote)

1. SSR marker (say SSR1) should be polymorphic between parents.

2. Only those plants who are real F1's will show double band when you use SSR1.

3. The best method is conventional breeding (art with science). Grow your F1's in between parents. An experienced breeder will identify F1 in field.

only reliable ssr (co-dominant) markers which are showing polymorphic between homozygous parents will produce double bands in F1.

ssr markers which are polymorphic between parents but not producing double bands in F1 is a case where that specific ssr markers not reliable marker or F1 seed is not a hybrid seed.

Fi population is always heterozygous whatever the marker system you are using. if you like to identify inheritances of character then you need F3 to F5 population 

Yes,  true F1s will always show double band(heterozygous) if you are using parental polymorphic Codominant type Marker.