The aya doesn't mean that thunder is an angel:
وَيُسَبِّحُ الرَّعْدُ بِحَمْدِهِ وَالْمَلَائِكَةُ مِنْ خِيفَتِهِ
وَيُرْسِلُ الصَّوَاعِقَ فَيُصِيبُ بِهَا مَنْ يَشَاءُ
And the thunder declares His glory with His praise, and the angels too
for awe of Him; and He sends the thunderbolts and smites with them
whom He pleases, yet they dispute concerning Allah, and He is mighty
The aya means that the thunder declares the glory of Allah and his praise. That doesn't imply that the thunder is an angel. It's like in the aya:
Do you not see that to Allah prostrates whoever is in the heavens and
whoever is on the earth and the sun, the moon, the stars, the
mountains, the trees, the moving creatures and many of the people? But
upon many the punishment has been justified. And he whom Allah
humiliates - for him there is no bestower of honor. Indeed, Allah does
what He wills. 22/18
The seven heavens and the earth and whatever is in them exalt Him. And
there is not a thing except that it exalts [ Allah ] by His praise,
but you do not understand their [way of] exalting. Indeed, He is ever
Forbearing and Forgiving. 17/44
Here, the Sun and the Moon and trees are not angels, yet they prostrate to Allah. But we don't know this can be not like our sujud (prostrates).
As for the hadith, I read that this hadith is authentic on some websites, and I read that is not in some others. We need a student of Hadith terminology to tell us.
I found some explication of this is hadith. I can't translate it, but one of them of ibn-taymya. It's awesome (may someone translate for us):
يقول شيخ الإسلام ابن تيمية في معنى الحديث :
وقد روي عن بعض السلف أقوال
لا تخالف ذلك، كقول من يقول إنه (أي الرعد) اصطكاك أجرام السحاب بسبب
انضغاط الهواء فيه، فإن هذا لا يناقض ذلك لأن الرعد مصدر رعد يرعد رعداً،
وكذلك الراعد يسمى رعداً، كما يسمى العادل عدلاً، والحركة توجب الصوت،
والملائكة هي التي تحرك السحاب وتنقله من مكان إلى مكان، وكل حركة في
العالم العلوي والسفلي فهي عن الملائكة.
He said that some scholars of Salaf (older scholars than him) gave a scientific explication to thunder (as air compression, and things like that). He said that this scientific explication doesn't conflict the explication in hadith because of a language-related reason. (He explains it, but I can't translate it.)
I say: this hadith might be authentic or might be not, and even if it's authentic that doesn't mean we don't believe in science. Like, in death, science gives us what he sees. And we know that there is angel of spirits that take our spirits out of our bodies.