Holden has written about donation restrictions on the GiveWell blog back in 2009 (bold and italics in original):

• We would guess that cases fitting the conditions for “meaningful restricted funding” are rare – i.e., when you give to a multiprogram organization, your donation usually will expand what they want to expand, regardless of how you restrict it.
• We have a general aversion to restricting donations. It seems like “micromanaging” an organization in this way is asking for trouble: the charity may avoid your intentions using technicalities or spend the “extra money” allocated to a program badly, and in any case, you are creating an extra headache for the charity.

Thus, our current rule of thumb is to find an organization whose existing priorities you are comfortable with – and give unrestricted.

See also the following on the GiveWell blog:

• The comments by GiveWell analysts Alexander Berger and Timothy Telleen-Lawton on giving to GiveWell in this recent post.
• Holden's post on GiveWell's funding needs in 2013 where he asked more donors to donate unrestricted to GiveWell. (For their latest budget and revenue forecasts, see this document from September.)