>>I started to see bees with small...deformed wings held parallel and tightly  against the abdomen.

A classic symptom of varroa-vectored virus.  Such deformed wings are common in treated colonies starting in August when the varroa population is reaching a peak.

I had a similar observation which may possibly be attributable to a different cause.  I had a number of feral brood combs that were exposed to cold temps around 50F for several hours.  When I got home I placed the combs in an empty box and shook in the bees from my bee vac.  I inspected a week and a half later and saw a few young bees with deformed wings.

I was surprised because I did not see any deformed wings or varroa when I collected these bees.  I went through the feral combs very thorougly during the inspection looking for varroa - usually very easy to spot when deformed wings are seen - but did not see a single varroa.

Here are my questions:

1. Can exposure to cold arrest pupae development and result in deformed wings?

2. Can the deformed wing virus spread by means other than varroa?

>>The colony had a good but not outstanding working field force

Varroa affects the longevity of the bees.  It takes a while for the numbers to recover in a sustainable way.

>>If this is deformed wing virus, should I destroy the colony?

I would not.  If you have beat varroa back, the colony should recover and be fine until you reach the next varroa pop. peak.

>>What happens if the queen has the virus?

I have not heard that varroa goes after the queen.  Perhaps they are less attracted to her scents.

Waldemar

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