Sue Bruce Wayne for funding him and assisting in a violation of said criminal's civil rights, under the doctrine of "respondeat superior."
Actually, respondiat superior doesn't apply to independent contractors. As long as Bruce Wayne doesn't order Batman to do anything, he isn't liable. But, you're right, it leaves him vulnerable to discovery and all that stuff.
The problem is that Bruce is going to have a hard time convincing people Batman is an independent contractor (assuming he even is one: if your employer provides you a workspace, sets your hours and pays your salary, you're an employee, not an independent contractor).
Yeah, maybe, after several years of pretrial proceedings, Bruce will convince a judge that Batman is not actually an employee of his. But as you note the discovery will have to occur first.
Also, just because someone's an "independent contractor" doesn't mean there aren't legal ramifications.
The IRS is going to want to know why Bruce hasn't been filing 1099 forms for all those independent contractors.
And speaking of the IRS:
My adult self will assume that the company was compensated from Bruce's private accounts for any and all material developed by Wayne Tech/Industries/Enterprises.
So, Bruce's tax returns--and the Wayne tax returns--show that?
And Bruce's returns also show all the "unofficial" compensation he received over the years while stealing the tech?
Sh'yeah. Right.
Basically, like Al Capone, the feds now have Batman on tax fraud.
Not to mention securities fraud. Because even if Bruce repaid the company after getting caught, he still committed fraud before that.
Lex Luthor? Bruce is more like the DCU version of Gordon Gekko at this point.