Is saving data to WordPress options as array bad thing to do?

It depends, if you use the data, only as a whole. Lets say for configuration settings or something, then I would say, it’s not a problem. But if you are doing queries on the data, like searching or fetching only 1 or 2 fields from that array.. you should use other solutions.

If you are missing some values from your array, are you sure these values are submitted from your form? (Are the fields not “disabled”, or are these fields unchecked checkboxes?)