Yeah well it creates the plothole in that they could have attacked the Lucifer earlier...they would have realized that its shields did not work in subspace as well...
Theories are meant to fix plotholes not make new ones. 
Indeed, s-99's theory breaks what we've been discussing this past week

Most likely, if one was in subspace along with other ships, you would be able to target them normally, as shown in Good Luck (and in Derelict. I'm not about to let a bunch of debris floating in a node ruin this little subspace theory we're discussing.)
As far as I'm concerned, even though established canon is what is contained in the

documentation and games, I consider Derelict and ST:R to be semi-canon. Derelict holds up as an addition to the FS storyline(as discussed here), and ST:R, being made by the ones who actually work and develop on FSO, is to be a good replacement to the weak, original ST.
I plan to contribute on the wiki extensively over the next couple weeks and I will respect canon in my additions, but I submit we consider that some campaigns have grounds to be considered semi-canon.
Maybe a new thread is in order?