Like everything else in social media, it depends.
Our state agency (mdc.mo.gov) keeps everything in one account, but we are fairly focused in our mission and reach the most people that way. One Facebook page, one Twitter account. Our regions and facilities are too small to justify the amount of time and energy needed to maintain the beast.
For other agencies, especially at the federal level, it makes sense to segment out your markets. I wouldn't want to follow the USGS, but I may want to follow their earthquake tweets or their hydrography tweets. If you can establish that there is a market for another Twitter account, then go for it. You can even start it and monitor it; if the keepers don't post, or it doesn't get any followers, kill it.
If you are a state agency with a broad focus, it may make sense to have multiple accounts. Missouri's economic development agency does tourism, business development, etc. These are discrete audiences, so it makes sense to have separate Twitter accounts for each one.