I think they can still get paid pretty well for them. For one, if these releases occur, they're better than nothing; right now, media companies derive no advertising revenue from torrented files with ads embedded because they don't offer them at all. Even if they have to sell for a reduced price, that's better than zero.
Furthermore, "skipping the ads" isn't that big of a deal. People do it on TV all the time by getting up to go do something else, changing the channel, muting the television, etc., when the commercials play. Those with DVRs or VCRs fast-forward, as a VLC user might. VLC doesn't really offer much better fast-forward features than the VCR; unless you also download a pre-defined chapter file (and I don't think many people hate ads that much), this is no different than using DVR/VCR and there's no point in paying less for these ads. VLC users will still visually see your logos, commercial, etc., while watching and I think that has value too, and again, the situation in that respect is no different from conventional methods.
I think the real logistical issue here is that it'd be much more difficult to insert localized ads. Hulu et al can use IP geolocation to target local ads (I don't know if they do or not, but it's possible), but a nationally distributed mp4 file would only have nationally distributed advertisements. This causes some havoc on the current pricing system, as it cuts affiliates, who manage the advertisements on conventional TV, out of loop. Perhaps the corporate guys like this, but as long as terrestrial broadcasts are the predominant form of distribution, corporate is always going to be careful not to disrupt the affiliates' revenue stream too much.