Is the sentence correct "Programs are now can be deleted" ? The question is about verb "are", is it needed here? And if not, is it still acceptable to use it?
No and no. The three acceptable versions of these sentences are as follows:
The programs now can be run.
The programs now can be deleted.
The programs are now able to be run/deleted.
The use of "are" is neither needed nor grammatical unless connected with another word; in the last example, for instance, "are able" followed by the infinitive "to be."
You can say,
The programs are elegant/well designed/functioning properly,
*The programs are can be [anything].