There are reasons why transparent materials might have
to be more brittle than opaque ones: light doesn't easily pass through materials that have the sort of bonds that provide tensile strength. But this is by no means a universal given, and windows might easily be the strongest part of a starship, or then simply structurally identical to the opaque hull sections.
Aluminum as such is just an element you can insert in transparent and opaque materials; pure aluminum metal doesn't get transparent to visible light no matter what you do with it, but "transparent aluminum" does not have any "mandatory" physical properties we could infer from the name alone. For all we know, it doesn't even contain any aluminum at all, but is dubbed that because it is physically somewhat similar to aluminum metal, or for some other frivolous reason.