LNCS is no longer indexed in ISI's SCI. Instead, it is included in the ISI Proceedings list, which, together with their Web of Science, consitutes their Web of Knowledge, and which they consider to be their representative and comprehensive index for conference papers (whereas SCI(E) is thought of as the index focusing on journal papers).
In my opinion this is the correct thing to do: after all publishing in a conference is very different from publishing in a journal. Conference papers are shorter, they often contain partial results, and, in many conference, they are completed by follow-up journal versions. However, since in many universities the number of ISI-Web of Science indexed papers is important for promotion, the number of papers submitted for conferences may decrease; it may be the case of researchers choosing to submit their papers to ISI-Web of Science indexed journals (maybe with lower impact factor) instead of sending them to conferences.
Later edit: I have contacted Springer to ask what's it all about LNCS and ISI. Their answer was the following:
LNCS is no longer indexed in ISI's SCI. LNCS publications were phased out of the index as from October 2006, which means that there will not be an impact factor for 2006.
Thomson decided to make a greater distinction between conference proceedings and journal publications (not related to conferences). They decided to included LNCS, and other series consisting mainly of conference proceedings, in their ISI Proceedings list. LNCS is also listed in various other indexing and abstracting services such as DBLP, ZBlMath/CompuServe, core EI Compendex database, IO-Port, ACM Portal, Scopus, INSPEC, etc.
Although LNCS is now listed in ISI Proceedings, the series does constitute a lot more than "just" a proceedings series. For one thing, the papers presented at the conferences need to have passed through a stringent selection process, for another thing, we have an Editorial Board, the members of which are also involved in the selection process (of the conferences to be published in LNCS), and, in addition, many of our publications have a journal-like quality, such as the colored-cover sub-series (consisting of Festschrifts, State-of-the-Art Surveys, Tutorials, Hot Topics, and Dissertations) and the transactions sub-series. These contain lengthy and detailed papers, often by invited researchers. A small number of excellent monographs are also included.
We are aware that this is of no help whatsoever if Universities/funding institutions take inclusion in the SCI as the main criterion for academic promotion or research funding. Please note, however, that Springer has had no influence over this decision.