By "too much hassle" you mean that I can't have topics that I reply to automatically bookmarked? And other than that, the only difference between bookmarks and subscriptions is that I can't get e-mail notifications for bookmarked topics, and I can't not have e-mail notifications for subscribed topics? Other that that, those two features are exact duplicates of each other? If that's the case then I guess they could be integrated, but I don't think you should integrate them.
The only upside of the integration would be that you have the topics you want e-mail notification for and the topics you don't want e-mail notification for in a single list. Which may be more convenient for some users, but it may be less conventient for others. If you want to have notifications at all, then you probably have all the topics that you want to regularly check on the subscriptions list. And you don't want to check the bookmarked topics every time you check the subscribed ones. But if you don't want notifications at all, like me, then you just use the bookmarked list, problem solved. There may be users already who rely on both lists, using one for topics they want to check regularly, using the other for topics they just want to check out later.
A much better improvement than integration would be to just put an "Automatically bookmark topics that I start or reply to" option on the Edit posting defaults page in Board preferences. Also, rename "Notify me upon replies by default" to "Automatically subscribe to topics that I start or reply to". Or something similar, composed by someone who's first language is English.
And while we are on the topic of duplicates. I started a topic called "Monotheism is a political construct". It hasn't appeared yet. But now, that I moved my subscribed topics to the bookmark list, I noticed a topic called "Religion is a ruling class creation" that I never posted to, and I totally forgot about it. So if you could please catch that topic of mine before it appears and cancel it, we could have one less topics. Thanks.